AU2002340063B2

AU2002340063B2 - Novel cyclooxygenase variants and methods of use

Info

Publication number: AU2002340063B2
Application number: AU2002340063A
Authority: AU
Inventors: Vishvanath N. Chandrasekharan; Daniel Simmons
Original assignee: Brigham Young University
Current assignee: Brigham Young University
Priority date: 2001-09-28
Filing date: 2002-09-28
Publication date: 2007-05-10
Anticipated expiration: 2022-09-28
Also published as: WO2003029411A3; DE60238872D1; US20030220306A1; JP2005534279A; US20070065445A1; EP1463806B1; US7179627B2; CA2417455A1; ATE494363T1; EP1463806A4; US7601816B2; CA2417455C; EP1463806A2; WO2003029411A2

Abstract

The invention relates to the isolation of novel cyclooxygenase type 1 (COX-1) variant enzymes. More specifically, the invention relates to the identification of cyclooxygenase transcripts harboring inton 1, or fragment thereof, of cyclooxygenase 1. The invention further relates to the diagnosis of aberrant cyclooxygenase type 1 variant gene or gene product; the identification, production, and use of compounds which modulate cyclooxygenase type 1 variant gene expression or the activity of the cyclooxygenase type 1 variant gene product including but not limited to nucleic acid encoding cyclooxygenase type 1 variants and homologues, analogues, and deletions thereof, as well as antisense, ribozyme, triple helix, antibody, and polypeptide molecules as well as small inorganic molecules; and pharmaceutical formulations and routes of administration for such compounds.

Description

WO 03/029411 PCT/US02/30947 Novel Cyclooxygenase Variants and Methods of Use TECHNICAL FIELD [0001] This invention relates to novel nucleic acids encoding novel mammalian cyclooxygenase (Cox) polypeptides and methods of use therefore. The invention further relates to compounds that modulate Cox activity and methods of identifying such compounds.

CROSS REFERENCE TO RELATED APPLICATIONS (0002] This application claims priority from U.S. Provisional Application Serial No.

60/326,133, filed September 28, 2001, and from U.S. Provisional Application Serial No, 60/373,225, filed April 15, 2002, and from U.S. Provisional Application Serial No.

60/373,661, filed April 16,2002, and from U.S. Provisional Application Serial No.

60/41 1,57 5 filed September 16, 2002, which are incorporated herein by reference.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH (0003] This invention was made with government support under grant AR46688 awarded by the National Institutes of Health (NIH). The U.S. Government may have an interest in the subject matter of this patent application.

BACKGROUND

[0004] In eukaryotic cells, polyunsaturated fatty acids are oxygenated by three general systems: 1) cyclooxygenases (COXs) and related fatty acid oxygenases, including pathogeninducible oxygenases (PIOXs) identified in plants, animals and bacteria; 2) lipoxygenases; and 3) cytochrome P-450. Presently there are 2 COX isozymes known, COX-1 and COX-2.

The predicted amino acid sequences of COX-1 cloned in chicken and mammals possesses approximately 60% amino acid sequence identity with COX-2.

[00 0S The cyclooxygenation of arachidonic acid, catalyzed by two forms of cyclooxygenase produces prostaglandins which, in turn, regulate neurotransmission and immune and inflammatory responses by activating receptors coupled to cAMP formation.

(Goetzl et al., FASEB 9:1051, 1995). For example, inflammation is both initiated and maintained, at least in part, by the overproduction of prostaglandins in injured cells. The central role that prostaglandins play in inflammation is underscored by the fact that those aspirin-like non-steroidal anti-inflammatory drugs (NSAIDS) that are most effective in the

I

SUBSTITUTE SHEET (RULE 26) WO 03/029411 PCT/US02/30947 therapy of many pathological inflammatory states all act by inhibiting prostaglandin synthesis. NSAIDs are analgesic/antiinflammnatory/antipyretic medications that act as inhibitors of the cyclooxygenase active site of COX isozymes. Important mechanistic differences in the actions of individual NSAIDs with the COX active site exist. Of the NSAIDs in medical use, only aspirin is a covalent modifier of COX-1 and COX-2.

[0006] There is increasing emphasis on the development of compounds that modulate cyclooxygenase activity and methods for identifying such compounds. Therefore, there is a need for improved methods to study the effectiveness of existing anti-inflammatory drugs and to evaluate the effectiveness of potential anti-inflammatory agents, at the molecular level, as well as for reagents for use in such methods.

SUMMARY

[0007] The present invention is based, at least in part, on the discovery of novel nucleic acid molecules and polypeptides encoded by such nucleic acid molecules, referred to herein as cyclooxygenase type 1 (COX-1) variant proteins. A COX-1 variant nucleic acid molecules include those derived from the COX-1 genomic sequence and possessing intron 1. Similarly, a COX-1 variant amino acid sequence is encoded by a COX-1 variant nucleic acid sequence containing intron 1. COX-3 pCox-1), PCOX-la pCox-1A657) or PCOX-lb are examples of COX-1 variants encompassed by the invention. Further COX-1 variants include hCOX-3(cc) (human COX-3 derived from cerebral cortex), hCOX-3(af) (human COX-3 derived from lung cells), hCOX-3 (dellO) (human COX-3 derived from lung cells with exon deleted) and hCOX-3(cs) (human COX-3 consensus sequence). Such variants are useful for identifying compounds or agents that modulate the activity of a COX-1 variant.

Accordingly, in one aspect, this invention provides isolated nucleic acid molecules encoding COX-1 variant proteins or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection of COX-1 variantencoding nucleic acids.

[0008] In one embodiment, a COX-1 variant nucleic acid molecule of the invention comprises intron 1, or fragment thereof, of cycloxygenase type 1. In one aspect, the nucleic acid molecule is an mRNA transcript. In another aspect, the nucleic acid molecule is cDNA.

In another aspect, the nucleic acid molecule encodes a polypeptide comprising at least one domain that catalyzes the cyclization and/or oxygenation of an fatty acid radical, at least one membrane-binding domain, and at least one heme binding domain. In yet another aspect the WO 03/029411 PCT/US02/30947 nucleic acid molecule encodes a cyclooxygenase polypeptide, or naturally occurring allelic variant thereof, which comprises intron 1, or fragment thereof, of cyclooxygenase 1.

[0009] In another embodiment, the invention provides an isolated COX-1 variant polypeptide comprising an amino acid sequence encoded by intron 1, or fragment thereof, of cyclooxygenase 1, wherein the polypeptide catalyzes the oxygenation and/or cyclization of a fatty acid. In one aspect, the isolated polypeptide further comprises at least one membranebinding domain and at least one heme binding domain.

[0010] In another embodiment, a COX-1 variant nucleic acid molecule of the invention is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to a nucleotide sequence to the entire length of the nucleotide sequence) including SEQ ID NO:1, SEQ ID NO:3 COX-3) or a complement thereof. In another embodiment, a COX-1 variant nucleic acid molecule is 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% homologous to a nucleotide sequence including SEQ ID NO:4, SEQ ID NO:6 PCOXla), or a complement thereof. In another embodiment, a COX-1 variant nucleic acid molecule is 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% homologous to a nucleotide sequence including SEQ ID NO:7, SEQ ID NO:9 PCOX-lb), or a complement thereof.

In another embodiment, a COX-1 variant nucleic acid molecule is 60%, 65%, 70%, 85%, 90%, 95%, 98% homologous to a nucleotide sequence including SEQ ID hCOX-3(cc)), or a complement thereof. In another embodiment, a COX-1 variant nucleic acid molecule is 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% homologous to a nucleotide sequence including SEQ ID NO: 11 hCOX-3(af), or a complement thereof. In another embodiment, a COX-1 variant nucleic acid molecule is 60%, 65%, 70%, 75%, 90%, 95%, 98% homologous to a nucleotide sequence including SEQ ID NO:12 hCOX-3(dellO)), or a complement thereof. In yet another embodiment, a COX-1 variant nucleic acid molecule is 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% homologous to a nucleotide sequence including SEQ ID NO: 13 hCOX-3(cs)), or a complement thereof.

[0011] In one embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO:1 or 3, or a complement thereof. In another preferred embodiment, the nucleic acid molecule has the nucleotide sequence shown in SEQ ID NO: 1 or 3.

[0012] In another embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO:4 or 6, or a complement thereof. In another preferred embodiment, the nucleic acid molecule has the nucleotide sequence shown in SEQ ID NO:4 or 6.

WO 03/029411 PCT/US02/30947 [0013] In yet another embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO:10, or a complement thereof. In another embodiment, the nucleic acid molecule has the nucleotide sequence shown in SEQ ID [0014] In yet another embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO:11, or a complement thereof. In another embodiment, the nucleic acid molecule has the nucleotide sequence shown in SEQ ID NO:11.

[0015] In yet another embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO:12, or a complement thereof. In another embodiment, the nucleic acid molecule has the nucleotide sequence shown in SEQ ID NO:12.

[0016] In yet another embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO:13, or a complement thereof. In another embodiment, the nucleic acid molecule has the nucleotide sequence shown in SEQ ID NO:13.

[0017] In another embodiment, a COX-1 variant nucleic acid molecule includes a nucleotide sequence encoding a polypeptide having an amino acid sequence homologous to the amino acid sequence of SEQ ID NO:2 COX-3), SEQ ID NO:5 PCOX-la), SEQ ID NO:14 (hCOX-3(csl), SEQ ID NO:15 hCOX-3(cs2) and SEQ ID NO:16 hCOX-3(cs3). In a one embodiment, a COX-1 variant nucleic acid molecule includes a nucleotide sequence encoding a polypeptide having an amino acid sequence at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to an amino acid sequence including SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID NO:15 or SEQ ID NO:16 the entire amino acid sequence of SEQ ID NO:2, 5, 14, 15 or 16).

[0018] In one embodiment, an isolated nucleic acid molecule encoding the amino acid sequence of a COX-1 variant is derived from a mammalian source, for example, ovine, porcine, lupine or canine. In another embodiment, a COX-1 variant is derived from chicken.

In yet another embodiment, a COX-1 variant is derived from human.

[0019] Another embodiment of the invention features nucleic acid molecules, preferably COX-1 variant nucleic acid molecules, which specifically detect COX-1 variant nucleic acid molecules encoding a COX-1 variant polypeptide relative to nucleic acid molecules encoding non-COX-1 variant polypeptides. For example, in one embodiment, such a nucleic acid molecule is at least 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, or 800 nucleotides in length and hybridizes under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence shown in SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 13, or a complement thereof.

[0020] In other preferred embodiments, the nucleic acid molecule encodes a naturally occurring allelic variant of a polypeptide which includes the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule which includes SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 13 under stringent conditions.

Another embodiment of the invention provides an isolated nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 2, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising SEQ ID NO: 1 or 3 under stringent conditions; and b) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 5, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising SEQ ID NO: 4 or 6 under stringent conditions.

[0021] Another embodiment of the invention provides an isolated nucleic acid molecule that is antisense to a COX-1 variant nucleic acid molecule, the coding strand of a COX-1 variant nucleic acid molecule.

[0022] Another aspect of the invention provides a vector comprising a COX-1 variant nucleic acid molecule. In certain embodiments, the vector is a recombinant expression vector. In another embodiment, the invention provides a host cell containing a vector of the invention. The invention also provides a method for producing a protein or polypeptide, preferably a COX-1 variant protein or polypeptide, by culturing in a suitable medium, a host cell, a mammalian host cell or insect cell, of the invention containing a recombinant expression vector, such that the protein is produced.

[0023] Another aspect of this invention features isolated or recombinant COX-1 variant proteins and polypeptides. In one embodiment, the isolated protein, preferably a COX-1 variant protein COX-3, PCOX-la, hCOX-3 hCOX-3 hCOX-3 (dellO) and hCOX-3 (cs) includes at least one domain that catalyzes the cyclization and/or oxygenation of an fatty acid radical, at least one membrane-binding domain, and at least one heme binding domain. In another embodiment, the isolated protein, preferably a COX-1 variant protein, includes at least one domain that catalyzes the cyclizationand/or oxygenation of an fatty acid radical, at least one membrane-binding domain, at least one [RALIBT]52757.doc:LNB heme binding domain, and has an amino acid sequence which is at least 50%, 55%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to an amino acid sequence including SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16. In another embodiment the present invention provides an isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 2, 5, 14, 15 or 16. In yet another embodiment, the isolated protein, preferably a COX-1 variant protein, includes at least one domain that catalyzes the cyclizationand/or oxygenation of an fatty acid radical, at least one membrane binding domain, at least one heme binding domain, and is expressed and/or functions in cells of the central nervous system. In an even further 0o embodiment, the isolated protein, preferably a COX-1 variant protein, includes at least one domain that catalyzes the cyclization and/or oxygenation of an fatty acid radical, at least one membrane-binding domain, at least one heme binding domain and plays a role in signalling pathways associated with cellular growth, signalling pathways associated with cell cycle regulation and central nervous system function. In another embodiment, the isolated protein, preferably a COX-1 variant protein, includes at least one domain that catalyzes the cyclization and/or oxygenation of an fatty acid radical, at least one membrane-binding domain, at least one heme binding domain, and is encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 13.

[0024] In another embodiment, the isolated protein has an amino acid sequence homologous to the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16. In one embodiment, the protein has an amino acid sequence at least about 50%, 55%, 60%, 65%, 70%, 75%,80%, 85%, 90%, 98% or more homologous to an amino acid sequence including SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16, the entire amino acid sequence of SEQ ID NO: 2, 5, 14, 15 or 16). In another embodiment, the invention features fragments of the proteins having the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16, wherein the fragment comprises at least 15 amino acids contiguous amino acids) of the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16. In another embodiment, the protein has the amino acid sequence of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16.

R:LIBT]52757.doc:LNB [0025] Another embodiment of the invention features an isolated protein, preferably a COX-1 variant protein, which is encoded by a nucleic acid molecule having a nucleotide sequence at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to a nucleotide sequence to the entire length of the nucleotide sequence) including SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 13, or a complement thereof. This invention further features an isolated protein, preferably a COX-1 variant protein, which is encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising to the nucleotide sequence of SEQ ID NO: 1, SEQ ID NO: 3,SEQ ID NO: 4,SEQ ID NO: 6,SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 13, or a complement thereof.

[0026] The proteins of the present invention or biologically active portions thereof, can be operatively linked to a non-COX-1 variant polypeptide heterologous amino acid sequences) to form fusion proteins. The invention further features antibodies, such as monoclonal or polyclonal antibodies, that specifically bind proteins of the invention, preferably COX-1 variant proteins COX-3, PCOX-la, PCOXlb, hCOX-3 (cc), hCOX- 3 hCOX-3 (dell0) or hCOX-3 In addition, the COX-1 variant proteins or biologically active portions thereof can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.

[0027] In another embodiment, the present invention provides a method for detecting the presence of aCox-1 variant nucleic acid molecule, protein or polypeptide in a biological sample by contacting the biological sample with an agent capable of detecting a COX-1 variant nucleic acid molecule, protein or polypeptide such that the presence of a COX-1 variant nucleic acid molecule, protein or polypeptide is detected in the biological sample.

[0028] In another embodiment, the present invention provides a method for detecting the presence of COX-1 variant activity in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of COX-1 variant activity such that the presence of COX-1 variant activity is detected in the biological sample.

[0029] In another aspect the invention provides a method for identifying a compound that modulates the activity of a COX-1 variant protein or nucleic acid by providing an indicator composition comprising a COX-1 variant protein having COX-1 variant activity, contacting the indicator composition with a test compound, and determining the effect of the test compound on COX-1 variant activity in the indicator composition to identify a compound that modulates the activity of a COX-1 variant protein.

[R:\LIBT]52757.doc:LNB [0030] In another aspect, the invention provides a method for modulating COX-1 variant activity comprising contacting a cell capable of expressing COX-1 variant with an agent that modulatesCOX-1 variant activity such that COX-I variant activity in the cell is modulated.

In one embodiment, the agent inhibits COX-1 variant activity. In another embodiment, the agent stimulates COX-1 variant activity. In one embodiment, the agent is an antibody that specifically binds to a COX-1 variant protein. In another embodiment, the agent modulates expression of a COX-1 variant by modulating transcription of a COX-I variant gene or translation of a COX-1 variant mRNA. In yet another embodiment, the agent is a 1o nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of a COX-1 variant mRNA or a COX-1 variant gene.

[0031] In one embodiment, the methods of the present invention are used to treat a subject having a disorder characterized by aberrant COX-1 variant protein or nucleic acid expression or activity by administering an agent that is a COX-1 variant modulator to the Is subject. In one embodiment, the COX-1 variant modulator is a COX-I variant protein. In another embodiment the COX-1 variant modulator is a COX-1 variant nucleic acid molecule.

In yet another embodiment, the COX-1 variant modulator is a peptide, peptidomimetic, or other small molecule. In a preferred embodiment, the disorder characterized by aberrant COX-I variant protein or nucleic acid expression is a cellular growth related disorder, a neoplastic disorder, or a disorder of the central nervous system, Alzheimer's Disease.

In another embodiment, the present invention provides a method for preventing or treating Alzheimer's Disease in a subject, said method comprising administering to said subject an effective amount of a specific inhibitor of COX-1 variant activity, in a pharmaceutically acceptable carrier.

In yet another embodiment, the present invention provides a method for treating immune or inflammatory conditions associated with Alzheimer's Disease in a subject, said method comprising administering to said subject a specific inhibitor of a COX-1 variant activity, in a pharmaceutically acceptable carrier.

In another embodiment, the present invention provides a method of modulating expression, production, or formation of amyloid precursor protein (APP) in a subject, comprising administering to said subject an effective amount of an antagonist, wherein said antagonist is a non-steroidal anti-inflammatory agent that is a specific inhibitor of a COX-1 variant, in a pharmaceutically acceptable carrier.

[R:\LIBT]52757.doc:LNB [0032] The present invention also provides a diagnostic assay for identifying the presence or absence of a genetic alteration characterized by at least one of aberrant modification or mutation of a gene encoding a COX-1 variant protein; (ii) mis-regulation of the gene and (iii) aberrant post-translational modification of a COX-1 variant protein, wherein a wild-type form of the gene encodes a protein with a COX-1 variant activity. A diagnostic assay can include, for example, an array-based system for detecting the presence or absence of a COX1 variant or the presence or absence of a genetic alteration in a COX-1 variant.

[0033] In another embodiment, the invention provides a method for ameliorating a neurodegenerative condition in a subject by administering a specific inhibitor ofa COX-1 variant encoded by a nucleic acid as set forth in the present invention, in a pharmaceutically acceptable carrier.

[0034] In another embodiment, the invention provides a method for selectively inhibiting COX-3, PCOX-la, PCOXlb, hCOX-3 (cc),hCOX-3 hCOX-3 (dell0) or hCOX-3 (cs) activity in a subject by administering a compound that selectively inhibits activity of the COX-3, PCOX-la, PCOXlb, hCOX-3 hCOX-3 hCOX-3 (dellO) or hCOX- 3 (cs) gene product to a subject in need of such treatment.

[0035] In another embodiment, the invention provides a method for selectively inhibiting COX-3, PCOX-la, PCOXlb, hCOX-3 hCOX-3 hCOX-3 (dell0) or hCOX-3 (cs) activity in a subject by administering a non-steroidal compound that selectively inhibits activity of the COX-3, PCOX-la, PCOXlb, hCOX-3( cc), hCOX-3 hCOX-3 (dellO) or hCOX-3 (cs) gene product in a subject in need of such treatment, wherein the activity of the non-steroidal compound does not result in significant toxic side effects in the subject.

[0036] In yet another embodiment, the invention provides a method for selectively inhibiting COX-1 variant activity in a subject by administering a non-steroidal compound that selectively inhibits activity of a COX-1 variant gene product in a subject in need of such treatment, wherein the ability of the non-steroidal compound to selectively inhibit the activity of the COX-1 variant gene product is determined by contacting a genetically engineered cell that expresses, for example, COX-3, PCOX-la, PCOXlb, hCOX-3 (cc), hCOX-3 hCOX- 3 (dellO) or hCOX-3 and not COX-1 or COX-2, with the compound and exposing the cell to a pre-determined amount of arachidonic acid; contacting a genetically engineered cell that expresses COX-1 or COX-2, and not a COX- 1 variant, with the compound and exposing the cell to a pre-determined amount of arachidonic acid; measuring the conversion of arachidonic acid to its prostaglandin [R:\LIBT]52757.doc:LNB metabolite; and comparing the amount of the converted arachidonic acid converted by each cell exposed to the compound to the amount of the arachidonic acid converted by control cells that were not exposed to the compound, so that the compounds that inhibit a COX-I variant activity and not COX-1 or COX-2 activity are identified.

In another embodiment the present invention provides a method for selectively inhibiting COX-3 or PCOX-la activity in a subject, comprising administering a non-steroidal compound that selectively inhibits activity of the COX-3 or PCOX-la gene product in a subject in need of such treatment, wherein the ability of the non-steroidal compound to selectively inhibit the activity of the COX-3 or PCOX-la gene product is determined by: a) contacting a genetically engineered cell that expresses COX-3 or PCOX-la, and not COX-1 or COX-2, with the compound and exposing the cell to a pre-determined amount of arachidonic acid; b) contacting a genetically engineered cell that expresses COX-1 or COX-2, and not COX-3 or PCOX-la, with the compound and exposing the cell to a predetermined amount of arachidonic acid; c) measuring the conversion of arachidonic acid to its prostaglandin metabolite; and d) comparing the amount of the converted arachidonic acid converted by each cell exposed to the compound to the amount of the arachidonic acid converted by control cells that were not exposed to the compound, so that the compounds that inhibit COX-3 or PCOX-la and not COX-1 or COX-2 activity are identified.

In another embodiment the present invention provides a method of identifying a compound that modulates the activity of COX-1 variant, the method comprising: a) providing a cell transfected with a DNA encoding a COX-1 variant, wherein the DNA comprises intron 1 of a cyclooxygenase type 1, and wherein the cell expresses COX-1 variant; b) contacting said cell, in an intact or disrupted state, with a test compound; and c) determining whether the activity of COX-1 variant is decreased or increased in the presence of the test compound, wherein a decrease or increase in said COX-1 variant activity is an indication that the test compound modulates the activity of a COX-1 variant.

An article of manufacture comprising packaging material and, contained within the packaging material, a compound that modulates the activity of COX-1 variant wherein the DNA encoding a COX-1 variant comprises intron 1 of a cyclooxygenase type 1, wherein the packaging material comprises a label or package insert indicating that said compound modulates the activity of a COX-1 variant and can be used for treating pain in a subject.

An article of manufacture comprising packaging material and, contained within the packaging material, a compound that modulates the activity of COX-1 variant wherein the DNA encoding a COX-1 variant comprises intron 1 of a cyclooxygenase type 1, wherein [R:\LIBT]52757.doc:LNB the packaging material comprises a label or package insert indicating that said compound modulates the activity of a COX-1 variant and can be used for treating inflammation in a subject.

An article of manufacture comprising packaging material and, contained within the s packaging material, a compound that preferentially modulates the activity of a COX-1 variant wherein the DNA encoding a COX-1 variant comprises intron 1 of a cyclooxygenase type 1, in comparison to COX-1 or COX-2, wherein the packaging material comprises a label or package insert indicating that said compound modulates the activity of a COX-1 variant and can be used for treating a subject having a COX-1 associated disorder.

An array comprising a substrate having a plurality of addresses, wherein at least one address of said plurality of addresses comprises a capture probe that can specifically bind a COX-1 variant nucleic acid or a fragment of said COX-1 variant nucleic acid wherein the DNA encoding a COX-l variant comprises intron 1 of a cyclooxygenase type 1.

An array comprising a substrate having a plurality of addresses, wherein at least one address of said plurality of addresses comprises a capture probe that can specifically bind intron 1 ofa COX-I variant nucleic acid.

A method of selecting a therapy for a subject, the method comprising: a) obtaining a subject sample from a caregiver; b) obtaining a nucleic acid from the subject sample; c) identifying a subject expression profile from the nucleic acid; d) selecting from a plurality of reference profiles a matching reference profile most similar to the subject expression profile, wherein the reference profiles and the subject expression profile have a plurality of values, each value representing the expression level of a COX-1 variant; e) wherein each reference profile of the plurality of reference profiles is associated with a therapy; and f) transmitting a descriptor of the therapy associated with the matching reference profile to the caregiver, thereby selecting a therapy for said subject.

[0037] The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

Description of Drawings [0038] FigurelA depicts an alignment of known COX-2 sequences. "Guinea" represents guinea pig, "Rainbow" is rainbow trout, and "Brook" is brook trout. Asterisks are placed above cysteine residues that are known to be involved in disulfide bonding and [R:\LIBT]52757.doc:LN 9c gaps in the sequence are represented by a dash All numbering in these alignments uses the ovine sequence as a reference. Domains are indicated.

[0039] Figure 1B depicts an alignment of known COX-1 amino acid sequences for human (SEQ ID NO: 22), ovine (SEQ ID NO: 23), canine (SEQ ID NO: 24), bovine (SEQ ID s NO: 25), equine (SEQ ID NO: 26), rabbit (SEQ ID NO: 27), guinea (SEQ ID NO: 28), murine (SEQ ID NO: 29), rat (SEQ ID NO: 30), mink (SEQ ID NO: 30), chicken (SEQ ID NO: 31), rainbow trout (SEQ ID NO: 32), and brook trout (SEQ ID NO: 33).

Asterisks, dashes and alignment are the same as those indicated for FigurelA. Domains are indicated.

[0040] Figurel C depicts an alignment of the consensus amino acid sequences of COX-1 (SEQ ID NO: 34) and COX-2 (SEQ ID NO: 35) with the sequences of cyclooxygenases from Gersemia fruticosa (SEQ ID NO: 36) and Plexaura homomalla (SEQ ID NO: 37), which are [R:\LIBT52757.doc:LNB WO 03/029411 PCT/US02/30947 two species of coral. A period represents a residue for which no clear consensus (50% or greater) could be seen.

[0041] Figure 2 depicts the primary sequence alignment of the consensus cyclooxygenase sequences with three plant PIOXs isolated from rice (SEQ ID NO:38), A. Thaliana (SEQ ID NO:39), and tobacco (SEQ ID NO:40). The domains shown are for cyclooxygenase. Periods represent residues for which there is no consensus (less than 50% of known sequences have the same residue here). The signal peptide and EGF-like, binding, and dimerization domains are not present in the PIOX sequences. Additionally, the distal histidine is not present in the PIOX sequences. The "REHN" sequence is part of the peroxidase catalytic domain of cyclooxygenases, and represents a stretch of 9 amino acids that is absolutely conserved in all known cyclooxygenases. This sequence is degenerated in the PIOXs. The active site tyrosine and proximal histidine heme ligand are conserved in all of the PIOX sequences.

[0042] Figure 3 depicts activation of arachidonic acid by COX enzymes showing the essential role ofTyr385- an amino acid residue conserved in COXs and PIOXs. Step 1: Arachidonate is coordinated in the COX active site in an extended L shape, its carboxyl group being coordinated by ARG120 and TYR355. The Pro-S hydrogen from carbon 13 is abstracted by Tyr385 to form an arachidonyl radical. Step 2: Oxygen presumed to have diffused in to the COX active site through the mouth of the channel attacks the arachidonyl radical forming an endoperoxyl and cyclopentane ring. Step 3: The endoperoxyl radical is attacked by a second molecule of oxygen at carbon 15. Step 4: Tyr385 donates its hydrogen to form PGG2 and to reform the radical at Tyr385.

[0043] Figure 4 depicts a diagram of the catalytic cycle responsible for activation of Tyr 38 5 an amino acid residue conserved in COXs and PIOXs. An endogenous oxidant binds the peroxidase active site and oxidizes ferric heme to ferryl-oxo-porphyrin radical which in turn abstracts hydrogen from Tyr 385 to form a tyrosyl radical. Only one oxidation event at the peroxidase is needed to activate the enzyme, since the Tyr 385 radical is regenerated with each cyclooxygenase cycle.

[0044] Figure 5, panelA, depicts Northern blot analysis of the distribution of COX-1 in dog tissues. Arrows indicate additional COX-1 transcripts in brain tissue. S stomach; d duodenum; i ileum; j jejunum; c colon; 1= liver; s spleen; b brain; lu lung; o ovary; k kidney; m MDKC cells (ind). The blots were hybridized with 32 P-labeled canine COX-1 DNA (specific activity 8.8xl0 8 cpm/g ,6xlO0cpm/ml). Post hybridization washes were carried out for 3h with 3-4 changes in 2 x SSC/0.5%SDS at about 65 0

C.

WO 03/029411 PCT/US02/30947 [0045] Figure 5, panel depicts Northern blot analysis of the distribution of COX-1 in chicken tissues. Arrows indicate additional COX-1 transcripts in brain tissue. v seminal vesicle; p pancreas; t testicle; h heart; ly bursal lymph. The blots were hybridized as described for Figure 5, panel a).

[0046] Figure 5, panel C, depicts a Northern blot analysis of PCOX-1 COX-3) and PCOX-1A657 PCOXla) RNA.

[0047] Figure 6A depcits a nucleic acid sequence alignment of canine COX-1, PCOX-1 COX-3) and PCOX-1A657 PCOXla) and a consensus sequence.

[0048] Figure 6B depicts the predicted amino acid sequence of canine COX-1, PCOX-1 COX-3) and PCOX-1A657 PCOXla) as compared with a consensus sequence.

[0049] Figure 7 depicts an analysis of the structure of intron-1 of a COX-1 variant in human (SEQ ID NO:41) and mouse (SEQ ID NO:42) as compared with canine (SEQ ID NO:43). The human and mouse sequences contain an intron-1 that is similar in size to that in canine which, when retained, would provide an in-frame insertion into the signal peptide encoding the protein.

[0050] Figure 8 depicts a Northern blot analysis of canine total RNA (25ug) probed with 32 P-end labeled oligo (50mer) designed from within the first intron of COX-1 in canine. The blot was washed at a final stringency of Tm-4 (Tm calculated melting temperature). S stomach; D duodenum; I ileum; J =jejunum; C colon; L= liver; Sp spleen; Bm brain (cerebral cortex)- mRNA (2.5ug); Bt brain (cerebral cortex)- total RNA; Lu lung; O ovary; K kidney; Cl CC1 34 cells. The 5.2 kb mRNA that was detected in panels A,B and C and is designated by an arrow in Figure 8.

[0051] Figure 9A depicts the nucleotide coding sequence of COX-3.

[0052] Figure 9B depicts the amino acid sequence of a COX-3 polypeptide.

[0053] Figure 9C depicts the cDNA sequence of COX-3 transcript.

[0054] Figure 9D depicts the nucleotide coding sequence of PCOX-la.

[0055] Figure 9E depicts the amino acid sequence of PCOX-la polypeptide.

[0056] Figure 9F depicts the cDNA sequence of PCOX-lb transcript.

[0057] Figure 10, panel A, depicts a Northern blot analysis and RT-PCR of canine cerebral cortex poly(A) RNA (lane 1, 5.0 gg; lane 2, 2.5 igg) probed with 1) 32 P-labeled canine COX-1 cDNA fragment, 2) 32 P-labeled canine antisense oligonucleotide to intron 1 (CC).

[0058] Figure 10, panel B, depicts PCR amplification of PCOX-1 in canine cerebral cortex. Lane 1, ethidium bromide-stained gel of amplified products corresponding to PCOXla containing intron 1 (upper band) and PCOX- lb (lower band) lacking intron 1; lane 2, 11 WO 03/029411 PCT/US02/30947 Southern blot of the amplified products probed with antisense oligonucleotide (CCI) to intron 1; and lane 3, Southern blot using COX-3 cDNA as probe.

[0059] Figure 10, panel C, depicts human Multiple Tissue Northern blots (MTNR) probed with a 3 2 P-labeled human antisense oligonucleotide to intron 1 (HCI). The -5.2 kb mRNA was detected in blots 1-3 (adult tissues), and 4 (fetal tissues). Abbreviations: Am, amygdala; B, brain; C, cerebellum: Cc, cerebral cortex; Fl, frontal lobe; H, hippocampus; Ht, heart; K, kidney; L, lung; Li, liver; M, skeletal muscle; Md, medulla; N, caudate nucleus; Op, occipital pole; P, placenta; Pn, pancreas; Pu, putamen; Sc, spinal cord; T, thalamus; TI, temporal lobe; X, corpus callosum.

[0060] Figure 11 depicts a schematic representation of the domains of COX-3 and PCOX-1 in comparison to COX-1. Abbreviations: s, signal peptide; dl, dimerization domain/EGF-like domain 1; d2, dimerization domain 2; m, membrane binding domain; c, catalytic domain; i, 90 bp sequence encoded by intron 1.

[0061] Figure 12 depicts Western blots showing the expression of COX-3, PCOX-la and COX-1 in insect cells treated with and without tunicamycin (top panels). Arrows indicate glycosylated forms of COX-1 which are not present in cells treated with tunicamycin. Polyclonal antibodies to human and mouse COX-1 intron 1 sequence were used to probe the COX-3 and PCOX-la blots while a monoclonal antibody to ovine COX-1 (Cayman) was used to probe the mouse COX-1 blot. COX activity in insect cells expressing COX-3, PCOX-la, and COX-1. Cells were treated with and without tunicamycin (bottom panels).

[0062] Figure 13 depicts line graphs of drug inhibition studies showing the effects of acetaminophen (panel A and panel phenacetin (panel and dipyrone (panel D) on COX-1 COX-2 and COX-3 activity in insect cells. COX activity was measured by the formation of PGE 2 after exposure to exogenous 5 gM or 30 puM C, D) arachidonic acid for 10 minutes. Data are expressed as mean ±SEM 6-9).

[0063] Figure 14 depicts an alignment of the consensus sequences of COX-1, COX-2 and coral COX corresponding to structural helices H2, H5, and H8 with plant PIOXs and LDS.

The PIOXs are from Oryza sativa (rice), Arabidopsis thaliana (arabidopsis) and Nicotiana tabacum (tobacco). Also aligned is linoleate diol synthase from Gaeumannomyces graminis (LDS). The consensus is shown using small letters for >50% homology and capital letters for 100% homology. Periods indicate that <50% homology was seen.

WO 03/029411 PCT/US02/30947 [0064] Figure 15, panel A, depicts a Western blot of human aorta lysate probed with COX-1 and COX-3 antibodies. The blot (lanes 3-8, 20 ptg total aorta protein each lane) probed with primary, secondary, or blocked antibodies as indicated. A solid horizontal arrow indicates the 65 kDa protein, an open arrow indicates the 53 kDa proteins, and an upward diagonal solid arrow indicates the 50 kDa protein. A single asterisk denotes unglycosylated canine COX-3, and a double asterisk denotes unglycosylated canine PCOX-la.

[0065] Figure 15, panel B, depicts a densitometric analysis of 65, 53, and 50 kDa proteins. Percent relative densitometric units rdu) were calculated by comparison to the signal from unblocked primary antibodies. The 50kDa protein is not detected by unblocked or blocked COX-3 PAb.

[0066] Figure 16 depicts a comparison ofhCOX-3(cc), hCOX-3(af) and hCOX-3(dellO) cDNA and provides a hCOX-3(cs) consensus sequence (SEQ ID NO:13) which is a consensus sequence ofhCOX-3(af), hCOX-3(cc) and [0067] Figure 17 depicts the cDNA sequence ofhCOX-3(cc) transcript (SEQ ID [0068] Figure 18 depicts the cDNA sequence of hCOX-3(af) transcript (SEQ ID NO:11).

[0069] Figure 19 depicts the cDNA sequence of hCOX-3(dell 0) transcript (SEQ ID NO:12).

[0070] Figure 20A-F depicts consensus amino acid sequences (SEQ ID NO: 14, SEQ ID and SEQ ID NO:16) for different reading frames ofhCOX-3(cs) (SEQ ID NO:13).

[0071] Like reference symbols in the various drawings indicate like elements.

DETAILED DESCRIPTION [0072] The present invention is based, at least in part, on the discovery of novel molecules, referred to herein as "cyclooxygenase type 1 variants, "COX-1 variants" or "COX-1 variant nucleic acid and polypeptide molecules," which play a role in or function in signaling pathways associated with cell processes in brain and other tissues. Exemplary COX-1 variants of the invention include COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX- 3(af), hCOX-3 (dellO) and hCOX-3(cs). In one embodiment, the COX-1 variant molecules modulate the activity of one or more proteins involved in cellular growth or differentiation.

In another embodiment, the COX-1 variant molecules of the present invention are capable of modulating the function of the central nervous system.

[0073] Cyclooxygenase isozymes are the cellular targets of non-steroidal antiinflammatory drugs (NSAIDs), which include pharmaceutically-important therapeutic WO 03/029411 PCT/US02/30947 agents such as aspirin, ibuprofen, and naproxen. The present invention provides novel COX- 1 variant enzymes. Fatty acid oxygenase activity is central to the production of prostaglandins, thromboxanes, hydroxy- and hydroperoxy-fatty acids by cyclooxygenases and is also shared by a related group of enzymes, which in plants are called pathogen inducible fatty acid oxygenases (PIOXs). The present data indicate that PIOX-like enzymes are found widely in nature. PIOXs make hydroperoxy-fatty acids and their derivatives.

Thus, the present COX-1 variants, like PIOXs, contain the critical amino acid residues needed to synthesize important oxygenated fatty acid-derived messengers in the brain and in other tissue.

[0074] As previously noted, cyclooxygenases play a role in prostaglandin synthesis.

Inhibition or over stimulation of the activity of cyclooxygenases involved in signaling pathways associated with cellular growth can lead to perturbed cellular growth, which can in turn lead to cellular growth related disorders. As used herein, a "cellular growth related disorder" includes a disorder, disease, or condition characterized by a deregulation, an upregulation or a downregulation, of cellular growth. Cellular growth deregulation may be due to a deregulation of cellular proliferation, cell cycle progression, cellular differentiation and/or cellular hypertrophy. Examples of cellular growth related disorders include disorders such as cancer, melanoma, prostate cancer, cervical cancer, breast cancer, colon cancer, or sarcoma. Cellular growth related disorders further include disorders related to unregulated or dysregulated apoptosis programmed cell death). Apoptosis is a cellular suicide process in which damaged or harmful cells are eliminated from multicellular organisms.

Cells undergoing apoptosis have distinct morphological changes including cell shrinkage, membrane blebbing, chromatin condensation, apoptotic body formation and fragmentation.

This cell suicide program is evolutionarily conserved across animal and plant species.

Apoptosis plays an important role in the development and homeostasis ofmetazoans and is also critical in insect embryonic development and metamorphosis. Furthermore, apoptosis acts as a host defense mechanism. For example, virally infected cells are eliminated by apoptosis to limit the propagation of viruses. Apoptosis mechanisms are involved in plant reactions to biotic and abiotic insults. Dysregulation of apoptosis has been associated with a variety of human diseases including cancer, neurodegenerative disorders and autoimmune diseases. Accordingly, identification of novel mechanisms to manipulate apoptosis provides new means to study and manipulate this process.

[0075] The present invention is based, at least in part, on the discovery of novel molecules, referred to herein as COX-1 variant protein and nucleic acid molecules, which 14 WO 03/029411 PCT/US02/30947 comprise a family of molecules having certain conserved structural and functional features.

The term "family" when referring to the protein and nucleic acid molecules of the invention is intended to mean two or more proteins or nucleic acid molecules having a common structural domain or motif and having sufficient amino acid or nucleotide sequence homology as defined herein. Such family members can be naturally or non-naturally occurring and can be from either the same or different species. For example, a family can contain a first protein of human origin, as well as other, distinct proteins of human origin or alternatively, can contain homologues of non-human origin. Members of a family may also have common functional characteristics. One embodiment of the invention features exemplary COX-1 variants including COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs). The nucleic acid and protein molecules of the invention are described in further detail in the following subsections.

[0076] In one embodiment, a COX-1 variant nucleic acid molecules of the invention comprises intron 1, or fragment thereof, of cycloxygenase type 1. In one aspect, the nucleic acid molecule is an mRNA transcript. In another aspect, the nucleic acid molecule is cDNA.

In another aspect, the nucleic acid molecule encodes a polypeptide comprising at least one domain that catalyzes the cyclization and/or oxygenation of an fatty acid radical, at least one membrane-binding domain, and at least one heme binding domain. In yet another aspect the nucleic acid molecule encodes a cyclooxygenase polypeptide, or naturally occurring allelic variant thereof, which comprises intron 1, or fragment thereof, of cyclooxygenase 1.

[0077] The present invention provides nucleic acid molecules and polypeptides of COX-1 variants that possess a cyclooxygenase intron-1. Retention of intron-1 in these mRNA transcripts and cDNAs disrupts the signal peptide of the protein and, therefore, is predicted to change the subcellular localization of the proteins encoded by these mRNA transcripts and any cDNA derived therefrom. Changing the subcellular localization of these proteins from the lumen of the endoplasmic reticulum, where COX-1 is normally found, to the cytosol or other location will change posttranslational modifications, redox states, and protein-protein interactions of the proteins encoded by our cDNAs. These changes are predicted to have significant effect on the enzymatic activities of the proteins that will make them novel drug targets separate from COX-1.

[0078] Northern blot and RT-PCR data provided herein suggest that analogous sequences exist in humans. These data show that human tissues contain mRNAs encoded from the COX-1 gene that possess intron-1 sequences. Although cyclooxygenase intron-1 has been previously sequenced, the inventions disclosed herein provide the first evidence that intron-1 WO 03/029411 PCT/US02/30947 sequences are contained in mature cyclooxygenase transcripts. Alignment of these sequences shows that in each species intron one is short (90-102nt), the length of its sequence is a multiple of three, and the sequence is evolutionarily conserved. Because the sequence is a multiple of three, intron-1 constitutes an in-frame insertion when the sequence is retained in a COX-1 mRNA. The evolutionary conservation of the sequence predicts a conserved sequence encoded by the 5' end of the intron that is present in all 3 species and may be important in subcellular targeting of the protein.

[0079] An exemplary COX-1 variant includes COX-3. Northern blot analysis of (polyA) RNA from human tissues using an anti-sense oligonucleotide probe to intron 1 shows that a ~5.2 kb mRNA and, in some cases smaller mRNAs, are specifically detected by this probe.

Expression of this human -5.2 kb, intron-1-hybridizing RNA was highest in brain cortex, the same tissue which possesses a high amount of intron-1 containing COX-1 mRNA in dog.

The -5.2 kb RNA, from which COX-3 is expressed, was also found to be present in other parts of the brain and in other tissues such as heart and muscle. Reverse-transcriptasecoupled polymerase chain reaction (RT-PCR) using a primer pair consisting of a sense primer specific for intron-1 and an antisense primer to the region of the stop codon of the COX-1 open reading frame was performed using human brain RNA as template. This experiment produced a 1.8kb fragment, which is the correct size for amplification of human COX-1 cDNA containing intron-1. Moreover, hybridization of this blot with murine-COX-1 cDNA hybridized strongly at high stringency to the amplified fragment, demonstrating that this fragment contains human COX-1 cDNA.

[0080] In one embodiment, the isolated COX-1 variant proteins or polypeptides are identified based on the presence of at least one domain that catalyzes the cyclization and/or oxygenation of an fatty acid radical, at least one membrane-binding domain, and at least one heme binding domain.

[0081] Isolated proteins of the present invention have an amino acid sequence homologous to the amino acid sequence of COX-3, PCOX-la, hCOX-3(cc), hCOX-3(af), hCOX-3 (dell0) and hCOX-3(cs) or are encoded by a nucleotide sequence homologous to SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13. As used herein, the term "homologous" refers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent an amino acid residue which has a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences share common structural domains or motifs and/or a common functional activity. For example, amino acid or nucleotide sequences which share common structural domains have at least 30%, 40%, or 50% homology, N preferably 60% homology, more preferably 70-80%, and even more preferably 90-95% Shomology across the amino acid sequences of the domains and contain at least one and preferably two structural domains or motifs, and defined herein as sufficiently

C

homologous. Furthermore, amino acid or nucleotide sequences which share at least or 50%, preferably 60%, more preferably 70-80%, or 90-95% homology and share a common functional activity are defined herein as sufficiently homologous.

ND As used interchangeably herein a "COX-3", "biological activity of COX-3" or to "functional activity of COX-3", refers to an activity exerted by a COX-3 protein, c polypeptide or nucleic acid molecule on a COX-3 responsive cell or a COX-3 protein Ssubstrate, as determined in vivo, or in vitro, according to standard techniques. The CN biological activity of COX-3 is described herein. Similarly, "PCOX-la activity", "biological activity of PCOX-la" or "functional activity of PCOX-la", refers to an activity exerted by a PCOX-la protein, polypeptide or nucleic acid molecule on a PCOXla responsive cell or a PCOX-la protein substrate, as determined in vivo, or in vitro, according to standard techniques. The biological activity of PCOX-la is described herein. The previously described terms are applicable to all exemplary COX-1 variants described herein, including PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dell0) and hCOX-3(cs).

The nucleotide sequence of the isolated COX-3 cDNA and the predicted amino acid sequence of the COX-3 polypeptide are shown in Figures 9A (SEQ ID NO:1) and 9B (SEQ ID NO:2), respectively. The nucleotide sequence of the isolated PCOX-la cDNA and the predicted amino acid sequence of the PCOX-la polypeptide are shown in Figures 9D (SEQ ID NO:4) and 9E (SEQ ID NO:5), respectively. The consensus nucleotide sequence of hCOX-3(cc), hCOX-3(af) and hCOX-3(dellO) cDNA is shown in Figure 16 (SEQ ID NO:13). The nucleotide sequence of the isolated hCOX-3(cc) cDNA is shown in Figure 17 (SEQ ID NO:10). The nucleotide sequence of the isolated hCOX-3(af) cDNA is shown in Figure 18 (SEQ ID NO:11). The nucleotide sequence of the isolated hCOX-3(dellO) cDNA is shown in Figure 19 (SEQ ID NO:12). The amino acid sequences derived from the consensus sequence is shown in Figure 20A-F (SEQ ID NO:14, SEQ ID NO:15 and SEQ ID NO:16).

17 615442 IJIN One embodiment of the invention pertains to isolated nucleic acid molecules that

ID

0 encode proteins or biologically active portions thereof, as well as nucleic acid fragments Ci sufficient for use as hybridization probes to identify COX-1 variants COX-3, PCOX- Sla, hCOX-3(cc), hCOX-3(af), hCOX-3 (dell0) and hCOX-3(cs) -encoding nucleic acids mRNA) and fragments for use as PCR primers for the amplification or mutation of cI nucleic acid molecules. As used herein, the term "nucleic acid molecule" is intended to include DNA molecules cDNA or genomic DNA) and RNA molecules c mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. The N nucleic acid molecule can be single-stranded or double-stranded, but preferably is double- S 10 stranded DNA.

c An "isolated" nucleic acid molecule is one which is separated from other nucleic 0 acid molecules which are present in the natural source of the nucleic acid. For example, C with regards to genomic DNA, the term "isolated" includes nucleic acid molecules which are separated from the chromosomes with which the genomic DNA is naturally s1 associated. Preferably, an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated nucleic acid molecules can contain less than about 4kb, 3kb, 2kb, 1kb, 0.5kb or 0.lkb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived.

Moreover, an "isolated" nucleic acid molecule, such as a COX-1 variant cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.

A nucleic acid molecule of the present invention, a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. For example, using all or portion of the nucleic acid sequence of SEQ ID NO:1, or the nucleotide sequence of SEQ ID NO:3, as a hybridization probe, nucleic acid molecules can be isolated using standard hybridization and cloning 18 615442 1.JIN WO 03/029411 PCT/US02/30947 techniques as described in Sambrook, Fritsh, E. and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).

[0088] Moreover, a nucleic acid molecule encompassing all or a portion of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13 can be isolated by the polymerase chain reaction (PCR) using synthetic oligonucleotide primers designed based upon the sequence of SEQ ID NO: 1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, respectively.

[0089] A nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to COX-1 variant nucleotide sequences can be prepared by standard synthetic techniques, using an automated DNA synthesizer.

[0090] In various embodiments, an isolated nucleic acid molecule of the invention comprises the nucleotide sequence shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO: 13 corresponding to the coding region of COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs), respectively.

[0091] In another preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of the nucleotide sequence shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO: 13, or a portion of any of these nucleotide sequences. A nucleic acid molecule which is complementary to the nucleotide sequence shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, is one which is sufficiently complementary to the nucleotide sequence shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12 or SEQ ID NO:13, respectively, such that it can hybridize to the nucleotide sequence shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, respectively, thereby forming a stable duplex.

[0092] In still another preferred embodiment, an isolated nucleic acid molecule of the present invention comprises a nucleotide sequence which is at least about 50%, 54%, 62%, 65%, 70%, 75%, 78%, 80%, 85%, 86%, 90%, 95%, 97%, 98% or more WO 03/029411 PCT/US02/30947 homologous to the nucleotide sequence to the entire length of the nucleotide sequence) shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, or a portion of any of these nucleotide sequences.

[0093] Moreover, the nucleic acid molecule of the invention can comprise only a portion of the nucleic acid sequence of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, for example a fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of a protein. The nucleotide sequence determined from the cloning of the COX-1 variant transcript allows for the generation of probes and primers designed for use in identifying and/or cloning other COX-1 variant family members, as well as homologues from other species. The probe/primer typically comprises substantially purified oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12 or 15, preferably about 20 or 25, more preferably about 30,,35, 40, 45, 60, 65, or 75 consecutive nucleotides of a sense sequence of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, of an anti-sense sequence of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, or of a naturally occurring allelic variant or mutant of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13. In an exemplary embodiment, a nucleic acid molecule of the present invention comprises a nucleotide sequence which is at least 350, 400, 450, 500, 550, 600, 650, 700, 750, or 800 nucleotides in length and hybridizes under stringent hybridization conditions to a nucleic acid molecule of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13 [0094] As defined herein, nucleic acids that do not hybridize to each other under stringent conditions are still substantially homologous to one another if they encode polypeptides that are substantially identical to each other. This occurs, for example, when a nucleic acid is created synthetically or recombinantly using a high codon degeneracy as permitted by the redundancy of the genetic code.

[0095] Probes based on COX-1 variant nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins. In preferred embodiments, the probe further comprises a label group attached thereto, the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as a part of a diagnostic test kit for identifying cells or tissues which misexpress a COX-1 variant protein, such as by measuring a level of a COX-1 variant- WO 03/029411 PCT/US02/30947 encoding nucleic acid in a sample of cells from a subject detecting COX-1 variant nRNA levels.

[0096] A nucleic acid fragment encoding a "biologically active portion of a COX-1 variant protein" can be prepared by isolating a portion of the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, which encodes a polypeptide having a biological activity (the biological activities of the proteins are described herein), expressing the encoded portion of the protein by recombinant expression in vitro) and assessing the activity of the encoded portion of the protein.

[0097] The invention further encompasses nucleic acid molecules that differ from the nucleotide sequence shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, due to the degeneracy of the genetic code and, thus, encode the same proteins as those encoded by the nucleotide sequence shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12 or SEQ ID NO:13. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in SEQ ID NO:2, SEQ ID SEQ ID NO:14, SEQ ID NO:15 or SEQ ID NO:16.

[0098] In addition to the COX-1 variant nucleotide sequences shown in SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12 or SEQ ID NO:13, it will be appreciated by those skilled in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of the proteins may exist within a population the human population). Such genetic polymorphism may exist among individuals within a population due to natural allelic variation. As used herein, the terms "gene" and "recombinant gene" refer to nucleic acid molecules which include an open reading frame encoding a COX-1 protein, preferably a mammalian protein, and can further include non-coding regulatory sequences, and introns. Since natural allelic variations can arise in the COX-1 gene, variant nRNA transcripts encoding COX-1 variant polypeptides can include such allelic variations.

Any and all such nucleotide variations and resulting amino acid polymorphisms in COX-1 variant genes that are the result of natural allelic variation and that do not alter the functional activity of a COX-1 variant protein are intended to be within the scope of the invention.

[00991 Moreover, nucleic acid molecules encoding other COX-1 family members and, thus, which have a nucleotide sequence which differs from the sequences of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12 or SEQ ID NO:13, are intended to be within the scope of the invention. For example, 21 WO 03/029411 PCT/US02/30947 another COX-1 variant cDNA can be identified based on the nucleotide sequence of the disclosed human, canine or chicken sequences. Moreover, nucleic acid molecules encoding proteins of the invention from different species, and thus which have a nucleotide sequence which differs from the disclosed sequences of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13 are intended to be within the scope of the invention. For example, a mouse COX-1 variant cDNA can be identified based on the nucleotide sequence of a human, canine or ovine.

[00100 Nucleic acid molecules corresponding to natural allelic variants and homologues of the cDNAs of the invention can be isolated based on their homology to the COX-1 variant nucleic acids disclosed herein using the cDNAs disclosed herein, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions.

[00101] Accordingly, in another embodiment, an isolated nucleic acid molecule of the invention is at least 15, 20, 25, 30 or more nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12 or SEQ ID NO:13. In other embodiment, the nucleic acid is at least 30, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, or 600 nucleotides in length. As used herein, the term "hybridizes under stringent conditions" is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 30%, 40%, 50%, or homologous to each other typically remain hybridized to each other. Preferably, the conditions are such that sequences at least about 70%, more preferably at least about even more preferably at least about 85% or 90% homologous to each other typically remain hybridized to each other. Such stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley Sons, N.Y. (1989), 6.3.1-6.3.6. A preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45 0 C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65 0 C. Preferably, an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to the sequence of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13 corresponds to a naturally-occurring nucleic acid molecule. As used herein, a "naturally-occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature encodes a natural protein).

WO 03/029411 PCT/US02/30947 [00102] In addition to naturally-occurring allelic variants of the sequences that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequences of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:1l, SEQ ID NO:12 or SEQ ID NO:13, thereby leading to changes in the amino acid sequence of the encoded proteins, without altering the functional ability of the proteins. For example, nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues can be made in the sequence of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:ll, SEQ ID NO:12 or SEQ ID NO:13. A "non-essential" amino acid residue is a residue that can be altered from the wild-type sequence of the sequence of SEQ ID NO:2, SEQ ID SEQ ID NO:14, SEQ ID NO:15 or SEQ ID NO:16) without altering the biological activity, whereas an "essential" amino acid residue is required for biological activity. For example, amino acid residues that are conserved among the COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs) proteins of the present invention, are predicted to be particularly unamenable to alteration. Furthermore, additional amino acid residues that are conserved between the proteins of the present invention and other family members are not likely to be amenable to alteration.

[00103] Accordingly, another aspect of the invention pertains to nucleic acid molecules encoding proteins of the invention that contain changes in amino acid residues that are not essential for activity. Such proteins differ in amino acid sequence from SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID NO:15 or SEQ ID NO: 16, yet retain biological activity.

In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 41%, 42%, 45%, 50%, 55%, 59%, 60%, 65%, 70%, 75%, 80%, 81%, 85%, 90%, 95%, 98% or more homologous to the amino acid sequence of SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID NO:15 or SEQ ID NO:16, the entire amino acid sequence of SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID N015 or SEQ ID NO:16).

[00104 An isolated nucleic acid molecule encoding a protein of the invention which is homologous to the protein of SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID or SEQ ID NO: 16 can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, respectively, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into SEQ ID NO:1, SEQ 23 WO 03/029411 PCT/US02/30947 ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains lysine, arginine, histidine), acidic side chains aspartic acid, glutamic acid), uncharged polar side chains glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains threonine, valine, isoleucine) and aromatic side chains tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in a protein of the invention is preferably replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of a COX-1 variant coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for COX-1 variant biological activity to identify mutants that retain activity. Following mutagenesis SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13, the encoded protein can be expressed recombinantly and the activity of the protein can be determined.

[00105] In addition to the nucleic acid molecules encoding COX-3, PCOX-1a, hCOX- 3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs) proteins described above, another aspect of the invention pertains to isolated nucleic acid molecules which are antisense thereto.

An "antisense" nucleic acid comprises a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid. The antisense nucleic acid can be complementary to an entire COX-1 variant coding strand, or only to a portion thereof.

In one embodiment, an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence encoding a COX-1 variant. The term "coding region" refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding a protein of the invention. The term "noncoding region" refers to 5' and 3' 24 WO 03/029411 PCT/USO2/30947 sequences which flank the coding region that are not translated into amino acids also referred to as 5' and 3' untranslated regions).

[001061 Given the coding strand sequences encoding COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dell 0) and hCOX-3(cs) disclosed herein, antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of nRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, or 50 nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art.

For example, an antisense nucleic acid an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, phosphorothioate derivatives and acridine substituted nucleotides can be used. Examples of modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4-acetylytosine, (carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-Dmannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6isopentenyladenine, uracil-5-oxyacetic acid wybutoxosine, pseudouracil, queosine, 2thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, oxyacetic acid methylester, uracil-5-oxyacetic acid 5-methyl-2-thiouracil, 3-(3-amino-3- N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).

WO 03/029411 PCT/US02/30947 [00107] The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a protein to thereby inhibit expression of the protein, by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention include direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.

[00108] In still another embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave COX- 1 variant mRNA transcripts to thereby inhibit translation of mRNA. A ribozyme having specificity for a -encoding nucleic acid can be designed based upon the nucleotide sequence of a COX-1 variant cDNA disclosed herein SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13).

For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a -encoding mRNA. See, Cech et al. U.S. Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742. Alternatively, mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, Bartel, D.

and Szostak, J.W. (1993) Science 261:1411-1418.

[00109 Alternatively, COX-1 variant gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the the promoter WO 03/029411 PCT/US02/30947 and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See generally, Helene, C. (1991) Anticancer Drug Des. 6(6):569-84; Helene, C.

et al. (1992) Ann. N.Y. Acad. Sci. 660:27-36; and Maher, L.J. (1992) Bioassays 14(12):807- [00110] In yet another embodiment, the nucleic acid molecules of the present invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acid molecules can be modified to generate peptide nucleic acids (see Hyrup B. et al. (1996) Bioorganic Medicinal Chemistry 4 5-23). As used herein, the terms "peptide nucleic acids" or "PNAs" refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis ofPNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup B. et al. (1996) supra; Perry-O'Keefe et al.

Proc. Natl. Acad. Sci. 93: 14670-675.

S00111] PNAs of nucleic acid molecules disclosed herein can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, for example, inducing transcription or translation arrest or inhibiting replication. PNAs of the present nucleic acid molecules can also be used in the analysis of single base pair mutations in a gene, by PNA-directed PCR clamping); as 'artificial restriction enzymes' when used in combination with other enzymes, S1 nucleases (Hyrup B. (1996) supra)); or as probes or primers for DNA sequencing or hybridization (Hyrup B. et al. (1996) supra; Perry-O'Keefe supra).

[00112] In another embodiment, PNAs of a COX-1 variant can be modified, to enhance their stability or cellular uptake), by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras of COX-1 variant nucleic acid molecules can be generated which may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes, RNAse H and DNA polymerases), to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup B. (1996) supra). The synthesis of PNA-DNA 27 WO 03/029411 PCT/US02/30947 chimeras can be performed as described in Hyrup B. (1996) supra and Finn P.J. et al. (1996) Nucleic Acids Res. 24 3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry and modified nucleoside analogs, 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite, can be used as a between the PNA and the 5' end of DNA (Mag, M. et al. (1989) Nucleic Acid Res. 17: 5973-88). PNAmonomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn P.J. et al. (1996) supra).

Alternatively, chimeric molecules can be synthesized with a 5' DNA segment and a 3' PNA segment (Peterser, K.H. et al. (1975) Bioorganic Med. Chem. Lett. 5: 1119-11124).

[00113] In other embodiments, the oligonucleotide may include other appended groups such as peptides for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, Letsinger et al. (1989) Proc. Natl. Acad. Sci. US.

86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT Publication No. W088/09810) or the blood-brain barrier (see, PCT Publication No.

W089/10134). In addition, oligonucleotides can be modified with hybridization-triggered cleavage agents (See, Krol et al. (1988) Bio-Techniques 6:958-976) or intercalating agents. (See, Zon (1988) Pharm. Res. 5:539-549). To this end, the oligonucleotide may be conjugated to another molecule, a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization-triggered cleavage agent).

[00114] Another aspect of the invention pertains to isolated COX-1 variant proteins, and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise anti-COX-1 variant antibodies. In one embodiment, native pCox-1 and COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs) proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs) proteins are produced by recombinant DNA techniques. Alternative to recombinant expression, a COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs) protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.

[00115] An "isolated" or "purified" protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the COX-1 variant protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language "substantially free of cellular material" includes preparations of a COX-1 variant protein in which the protein is 28 WO 03/029411 PCT/US02/30947 separated from cellular components of the cells from which it is isolated or recombinantly produced. In one embodiment, the language "substantially free of cellular material" includes preparations of a COX-1 variant protein having less than about 30% (by dry weight) of nonprotein (also referred to herein as a "contaminating protein"), more preferably less than about of non- protein, still more preferably less than about 10% of non- protein, and most preferably less than about 5% non- protein. When the COX-1 variant protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation.

[00116] The language "substantially free of chemical precursors or other chemicals" includes preparations of a protein of the invention in which the protein is separated from chemical precursors or other chemicals that are involved in the synthesis of the protein. In one embodiment, the language "substantially free of chemical precursors or other chemicals" includes preparations of a COX-1 variant protein such as a COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs) protein having less than about (by dry weight) of chemical precursors or non- chemicals, more preferably less than about 20% chemical precursors or non- chemicals, still more preferably less than about chemical precursors or non- chemicals, and most preferably less than about 5% chemical precursors or non- chemicals.

[00117] Biologically active portions of a COX-1 variant protein include peptides comprising amino acid sequences sufficiently homologous to or derived from the amino acid sequence of the COX-1 variant protein, the amino acid sequence shown in COX-1 variant, which include less amino acids than the full length proteins, and exhibit at least one activity of a protein. Typically, biologically active portions comprise a domain or motif with at least one activity of the COX-1 variant protein. Abiologically active portion of a protein can be a polypeptide which is, for example, at least 10, 25, 50, 100 or more amino acids in length.

[00118] In a preferred embodiment, the COX-1 variant protein has an amino acid sequence shown in SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID N015 or SEQ ID NO:16.

In other embodiments, the COX-1 variant protein is substantially homologous to SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID NO15 or SEQ ID NO:16, and retains the functional activity of the protein of SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID or SEQ ID NO:16, yet differs in amino acid sequence due to natural allelic variation or 29 WO 03/029411 PCT/US02/30947 mutagenesis, as described in detail in subsection I above. Accordingly, in another embodiment, the COX-1 variant protein is a protein which comprises an amino acid sequence at least about 50%, 55%, 59%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:5 the entire amino acid sequence of SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:14, SEQ ID N015 or SEQ ID NO:16).

[00119] To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least even more preferably at least 60%, and even more preferably at least 70%, 80%, or 90% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid "identity" is equivalent to amino acid or nucleic acid "homology"). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.

00120 The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In a preferred embodiment, the percent identity between two amino acid sequences is determined using the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at http://www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.

[00121] The nucleic acid and protein sequences of the present invention can further be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using WO 03/029411 PCT/US02/30947 the NBLAST and XBLAST programs (version 2.0) ofAltschul, et al. (1990) J. Mol. Biol.

215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score 100, wordlength 12 to obtain nucleotide sequences homologous to nucleic acid molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score 50, wordlength 3 to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res.

25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov.

[001221 The invention also provides COX-1 variant chimeric or fusion proteins. As used herein, a "chimeric protein" or "fusion protein" comprises a COX-1 variant polypeptide operatively linked to a non-COX-1 variant polypeptide. An "COX-1 variant polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a COX-1 variant, including COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs), whereas a "non-COX-1 variant polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to a protein of the invention, a protein which is different from a COX-3, PCOX-la, PCOXlb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs) protein and which is derived from the same or a different organism. Within a COX-1 variant fusion protein the COX-1 variant polypeptide can correspond to all or a portion of a protein. In a preferred embodiment, a COX-1 variant fusion protein comprises at least one biologically active portion of a COX-1 variant protein. In another preferred embodiment, a COX-1 variant fusion protein comprises at least two biologically active portions of a COX-1 variant protein.

Within the fusion protein, the term "operatively linked" is intended to indicate that the COX- 1 variant polypeptide and the non- polypeptide are fused in-frame to each other. The nonpolypeptide can be fused to the N-terminus or C-terminus of the COX-1 variant polypeptide.

[00123] For example, in one embodiment, the fusion protein is a GST- fusion protein in which the sequences are fused to the C-terminus of the GST sequences. Such fusion proteins can facilitate the purification of recombinant COX-1 variants.

[00124] In another embodiment, the fusion protein is a COX-1 variant protein containing a heterologous signal sequence at its N-terminus. In certain host cells mammalian host cells), expression and/or secretion of a COX-1 variant can be increased through use of a heterologous signal sequence.

WO 03/029411 PCT/US02/30947 [00125] The fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject in vivo. The fusion proteins can be used to affect the bioavailability of a COX-1 variant substrate. Use of COX-1 variant fusion proteins may be useful therapeutically for the treatment of cellular growth related disorders or disorders associated with neurodegenerative disesaes. Moreover, the COX-1 variant -fusion proteins of the invention can be used as immunogens to produce anti- COX-1 variant antibodies in a subject, to purify ligands and in screening assays to identify molecules which inhibit the interaction of the enzyme with a substrate.

[0012 6] Preferably, a chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. John Wiley Sons: 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety a GST polypeptide). An encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the protein.

[00127 The present invention also pertains to variants of the COX-1 variant proteins which function as either COX-1 variant agonists (mimetics) or as COX-1 variant antagonists.

Variants of the COX-1 variant proteins can be generated by mutagenesis, discrete point mutation or truncation of a COX-1 variant protein. An agonist of the proteins can retain substantially the same, or a subset, of the biological activities of the naturally occurring form of a protein. An antagonist of a protein of the invention can inhibit one or more of the activities of the naturally occurring form of a protein of the invention by, for example, competitively modulating a cardiovascular system activity of a protein. Thus, specific biological effects can be elicited by treatment with a variant of limited function. In one embodiment, treatment of a subject with a variant having a subset of the biological activities WO 03/029411 PCT/US02/30947 of the naturally occurring form of the protein has fewer side effects in a subject relative to treatment with the naturally occurring form of the protein.

[00128] Apolypeptide "mutein" refers to a polypeptide whose sequence contains substitutions, insertions or deletions of one or more amino acids compared to the amino acid sequence of the native or wild type protein. A mutein has at least 50% sequence homology to the wild type protein, preferred is 60% sequence homology, more preferred is 70% sequence homology. Most preferred are muteins having 80%, 90% or 95% sequence homology to the wild type protein, in which sequence homology is measured by any common sequence analysis algorithm, such as Gap or Bestfit.

[00129] A "derivative" refers to polypeptides or fragments thereof that are substantially homologous in primary structural sequence but which include, in vivo or in vitro chemical and biochemical modifications or which incorporate unusual amino acids. Such modifications include but are not limited to, for example, acetylation, carboxylation, phosphorylation, glycosylation, ubiquitination, labeling, with radionuclides, and various enzymatic modifications, or conservative substitutions, as will be readily appreciated by those well skilled in the art. A variety of methods for labeling polypeptides and of substituents or labels useful for such purposes are well known in the art, and include radioactive isotopes such as 125, 32 P, 35, and 3 H, ligands which bind to labeled antiligands antibodies), fluorophores, chemiluminescent agents, enzymes, and antiligands which can serve as specific binding pair members for a labeled ligand. The choice of label depends on the sensitivity required, ease of conjugation with the primer, stability requirements, and available instrumentation. Methods for labeling polypeptides are well known in the art. See Ausubel et al., 1992.

[00130] In one embodiment, a modified COX-1 variant protein which function as either a COX-1 variant agonists (mimetics) or as COX-1 variant antagonists can be identified by screening combinatorial libraries of mutants, truncation mutants, of a COX-1 variant protein COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs)) agonist or antagonist activity. In one embodiment, a variegated library of modified COX-1 variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of modified COX-1 variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential COX-1 variant sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins for phage display) containing the set of COX-1 variant sequences therein.

33 WO 03/029411 PCT/US02/30947 There are a variety of methods which can be used to produce libraries of potential modified COX-1 variants from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential sequences. Methods for synthesizing degenerate oligonucleotides are known in the art (see, Narang, S.A. (1983) Tetrahedron 39:3; Itakura et al. (1984) Annu. Rev.

Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res.

11:477.

[0 0131] In addition, libraries of fragments of a COX-1 variants protein coding sequence can be used to generate a variegated population of COX-1 variants fragments for screening and subsequent selection of modified COX-1 variant protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of a COX-1 variant coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S1 nuclease, and ligating the resulting fragment library into an expression vector. By this method, an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes of the protein.

[00132] Several techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of COX-1 variant proteins. The most widely used techniques, which are amenable to high through-put analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recrusive ensemble mutagenesis (REM), a new technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify modified COX-1 variants (Arkin and Yourvan (1992) Proc. Natl.

Acad. Sci. USA 89:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331).

WO 03/029411 PCT/US02/30947 [00133] An isolated COX-1 variant protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind a COX-1 variant disclosed herein using standard techniques for polyclonal and monoclonal antibody preparation. A full-length protein can be used or, alternatively, the invention provides antigenic peptide fragments of, for example, COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs) for use as immunogens. The antigenic peptide of a COX-1 variant comprises at least 8 amino acid residues of the amino acid sequence shown in SEQ ID NO:2, SEQ ID SEQ ID NO:8, SEQ ID NO:14, SEQ ID N015 or SEQ ID NO:16, and encompasses an epitope of such that an antibody raised against the peptide forms a specific immune complex with. Preferably, the antigenic peptide comprises at least 10 amino acid residues, more preferably at least 15 amino acid residues, even more preferably at least 20 amino acid residues, and most preferably at least 30 amino acid residues.

[00134] Preferred epitopes encompassed by the antigenic peptide are regions of a COX-1 variant that are located on the surface of the protein, hydrophilic regions.

[00135] A COX-1 variant immunogen typically is used to prepare antibodies by immunizing a suitable subject, rabbit, goat, mouse or other mammal) with the immunogen. An appropriate immunogenic preparation can contain, for example, recombinantly expressed protein or a chemically synthesized COX-1 variant polypeptide.

The preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent. Immunization of a suitable subject with an immunogenic COX-1 variant preparation induces a polyclonal anti- antibody response.

[00136] Accordingly, another aspect of the invention pertains to anti- antibodies. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, molecules that contain an antigen binding site which specifically binds (immunoreacts with) an antigen, such as a COX-1 variant.

Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin. The invention provides polyclonal and monoclonal antibodies that bind a COX-1 variant. The term "monoclonal antibody" or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of a COX-1 variant.

A monoclonal antibody composition thus typically displays a single binding affinity for a particular COX-1 variant protein with which it immunoreacts.

WO 03/029411 PCT/US02/30947 [00137] Polyclonal anti- antibodies can be prepared as described above by immunizing a suitable subject with a COX-1 variant immunogen. The anti- antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized COX-1 variant. If desired, the antibody molecules directed against a COX-1 variant can be isolated from the mammal from the blood) and further purified by well-known techniques, such as protein A chromatography to obtain the IgG fraction. At an appropriate time after immunization, when the antiantibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497) (see also, Brown et al. (1981) J. Immunol. 127:539-46; Brown et al. (1980) J. Biol. Chem .255:4980- 83; Yeh et al. (1976) Proc. Natl. Acad. Sci. USA 76:2927-31; and Yeh et al. (1982) Int. J.

Cancer 29:269-75), the more recent human B cell hybridoma technique (Kozbor et al. (1983) Immunol Today 4:72), the EBV-hybridoma technique (Cole et al. (1985), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. The technology for producing monoclonal antibody hybridomas is well known (see generally R.

H. Kenneth, in Monoclonal Antibodies: ANew Dimension In Biological Analyses, Plenum Publishing Corp., New York, New York (1980); E. A. Lerner (1981) Yale J. Biol. Med., 54:387-402; M. L. Gefter et al. (1977) Somatic Cell Genet. 3:231-36). Briefly, an immortal cell line (typically a myeloma) is fused to lymphocytes (typically splenocytes) from a mammal immunized with a immunogen as described above, and the culture supematants of the resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds.

[00138 Any of the many well known protocols used for fusing lymphocytes and immortalized cell lines can be applied for the purpose of generating an anti- monoclonal antibody (see, G. Galfre et al. (1977) Nature 266:55052; Gefter et al. Somatic Cell Genet., cited supra; Lerner, Yale J. Biol. Med., cited supra; Kenneth, Monoclonal Antibodies, cited supra). Moreover, the ordinarily skilled worker will appreciate that there are many variations of such methods which also would be useful. Typically, the immortal cell line a myeloma cell line) is derived from the same mammalian species as the lymphocytes.

For example, murine hybridomas can be made by fusing lymphocytes from a mouse immunized with an immunogenic preparation of the present invention with an immortalized mouse cell line. Preferred immortal cell lines are mouse myeloma cell lines that are sensitive to culture medium containing hypoxanthine, aminopterin and thymidine ("HAT medium").

36 WO 03/029411 PCT/US02/30947 Any of a number of myeloma cell lines can be used as a fusion partner according to standard techniques, the P3-NSl/l-Ag4-1, P3-x63-Ag8.653 or Sp2/O-Agl4 myeloma lines.

These myeloma lines are available from ATCC. Typically, HAT-sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol Hybridoma cells resulting from the fusion are then selected using HAT medium, which kills unfused and unproductively fused myeloma cells (unfused splenocytes die after several days because they are not transformed). Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind, using a standard ELISA assay.

[00139] Alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal anti- antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library an antibody phage display library) with a COX-1 variant to thereby isolate immunoglobulin library members that bind a COX-1 variant. Kits for generating and screening phage display libraries are commercially available the Phannacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAPTM Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, Ladner et al. U.S. Patent No. 5,223,409; Kang et al. PCT International Publication No. WO 92/18619; Dower et al. PCT International Publication No. WO 91/17271; Winter et al. PCT International Publication WO 92/20791; Markland et al. PCT International Publication No. WO 92/15679; Breitling et al. PCT International Publication WO 93/01288; McCafferty et al. PCT International Publication No.

WO 92/01047; Garrard et al. PCT International Publication No. WO 92/09690; Ladner et al.

PCT International Publication No. WO 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J 12:725-734; Hawkins et al. (1992) J.

Mol. Biol. 226:889-896; Clarkson et al. (1991) Nature 352:624-628; Gram et al. (1992) Proc.

Natl. Acad. Sci. USA 89:3576-3580; Garrad et al. (1991) Bio/Technology 9:1373-1377; Hoogenboom et al. (1991) Nuc. Acid Res. 19:4133-4137; Barbas et al. (1991) Proc. Natl.

Acad. Sci. USA 88:7978-7982; and McCafferty et al. Nature (1990) 348:552-554.

[00140 Additionally, recombinant anti-COX-1 variant antibodies, such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention. Such chimeric and humanized monoclonal antibodies can be produced by 37 WO 03/029411 PCT/US02/30947 recombinant DNA techniques known in the art, for example using methods described in Robinson et al. International Application No. PCT/US86/02269; Akira, et al. European Patent Application 184,187; Taniguchi, European Patent Application 171,496; Morrison et al.

European Patent Application 173,494; Neuberger et al. PCT International Publication No.

WO 86/01533; Cabilly et al. U.S. Patent No. 4,816,567; Cabilly et al. European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl.

Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sun et al.

(1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al. (1987) Canc. Res. 47:999- 1005; Wood et al. (1985) Nature 314:446-449; and Shaw et al. (1988) J. Natl. Cancer Inst.

80:1553-1559); Morrison, S. L. (1985) Science 229:1202-1207; Oi et al. (1986) BioTechniques 4:214; Winter U.S. Patent 5,225,539; Jones et al. (1986) Nature 321:552-525; Verhoeyan et al. (1988) Science 239:1534; and Beidler et al. (1988) J. Immunol. 141:4053- 4060.

[00141] An anti-COX-1 variant antibody monoclonal antibody) can be used to isolate additional COX-1 variants, particularly those proteins retaining intron 1 of the COX-1 gene, by standard techniques, such as affinity chromatography or immunoprecipitation. An anti-COX-1 variant antibody can facilitate the purification of natural COX-1 variant from cells and ofrecombinantly produced COX-1 variant expressed in host cells. Moreover, an anti- antibody can be used to detect a COX-1 variant protein in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the COX-1 variant protein. Anti-COX-1 variant antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, -galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 1251, 131, 35 S or 3

H.

WO 03/029411 PCT/US02/30947 [00142 Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding a COX-1 variant protein (or a portion thereof). As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated.

Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques are often in the form ofplasmids. In the present specification, "plasmid" and "vector" can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors replication defective retroviruses, adenoviruses and adenoassociated viruses), which serve equivalent functions.

00143 The recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to includes promoters, enhancers and other expression control elements polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be WO 03/029411 PCT/US02/30947 transformed, the level of expression of protein desired, and the like. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein COX-1 variant proteins, modified forms of COX-1 variant proteins, fusion proteins, and the like).

[00144] The recombinant expression vectors of the invention can be designed for expression of COX-1 variant proteins in prokaryotic or eukaryotic cells. For example, COX- 1 variant proteins can be expressed in bacterial cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

[00145] Expression of proteins in prokaryotes is most often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S. (1988) Gene 67:31pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.

[00146] Purified fusion proteins can be utilized in COX-1 variant activity assays, direct assays or competitive assays described in detail below), or to generate antibodies specific for COX-1 variant proteins, for example.

[00147] Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pET lid (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) WO 03/029411 PCT/US02/30947 89). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET lid vector relies on transcription from a T7 gnl0-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident prophage harboring a T7 gnl gene under the transcriptional control of the lacUV 5 promoter.

[00148 One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 119-128). Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al., (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.

[00149] In another embodiment, the COX-1 variant expression vector is a yeast expression vector. Examples of vectors for expression in yeast S. cerevisiae include pYepSecl (Baldari, et al., (1987) Embo J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego, CA), and picZ (InVitrogen Corp, San Diego, CA).

[00150 Alternatively, COX-1 variant proteins can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells Sf9 cells) include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).

[00151] In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufnan et al.

(1987) EMBO J. 6:187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, Fritsh, E. and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.

WO 03/029411 PCT/US02/30947 00152] In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type tissuespecific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters ofT cell receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) and immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters milk whey promoter; U.S. Patent No. 4,873,316 and European Application Publication No.

264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the a-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).

[00153] The invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation.

That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to COX-1 variant mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced. For a discussion of the regulation of gene expression using antisense genes see Weintraub, H. et al., "Antisense RNA as a molecular tool for genetic analysis," Reviews Trends in Genetics, Vol. 1(1) 1986.

[00154] Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms "host cell" and "recombinant host cell" are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either WO 03/029411 PCT/US02/30947 mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

[00155] Ahost cell can be any prokaryotic or eukaryotic cell. For example, a COX-1 variant protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.

[00156 Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" are intended to refer to a variety of art-recognized teclmiques for introducing foreign nucleic acid DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), and other laboratory manuals.

[00157] For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding a pCox-1 or pCox-1A657 protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection cells that have incorporated the selectable marker gene will survive, while the other cells die).

[001581 Ahost cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce express) a COX-1 variant protein. Accordingly, the invention further provides methods for producing a COX-1 variant protein using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding COX-1 variant protein has been introduced) in a suitable medium such that a COX-1 variant protein is produced. In another embodiment, the method further comprises isolating a COX-1 variant protein from the medium or the host cell.

WO 03/029411 PCT/US02/30947 00159] The host cells of the invention can also be used to produce non-human transgenic animals. For example, in one embodiment, a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which -coding sequences have been introduced. Such host cells can then be used to create non-human transgenic animals in which exogenous COX-1 variant sequences have been introduced into their genome or homologous recombinant animals in which endogenous COX-1 variant sequences have been altered. Such animals are useful for studying the function and/or activity of a COX-1 variant such as COX-3, PCOXla, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs) and for identifying and/or evaluating modulators of their activity. A transgenic animal of the invention would include those animals that have been modified to express only a COX-1 variant protein (as opposed to co-expression of COX-1 and COX-1 variants). As used herein, a "transgenic animal" is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene.

Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like. A transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. As used herein, a "homologous recombinant animal" is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous COX-1 variant gene has been altered by homologous recombination between the endogenous gene and an exogenous DNAmolecule introduced into a cell of the animal, an embryonic cell of the animal, prior to development of the animal.

[00160] The nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more of the following methods: 1) screening assays; 2) predictive medicine diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenetics); and 3) methods of treatment therapeutic and prophylactic). The isolated nucleic acid molecules of the invention can be used, for example, to express COX-1 variant proteins via a recombinant expression vector in a host cell), to detect COX-1 variant mRNA in a biological sample), to modulate the activity ofprostaglandins, and to identify compounds that modify the activity of a COX-1 variant. For example, the COX-1 variant proteins can be used to treat disorders characterized by insufficient or excessive production of a substrate or production of COX-1 variant inhibitors. In addition, the proteins of the invention can be used to screen for naturally occurring cyclooxygenase substrates, to screen for drugs or compounds which modulate the activity of a COX-1 variant, as well as to 44 WO 03/029411 PCT/US02/30947 treat disorders characterized by insufficient or excessive production of a COX-1 variant protein. Moreover, the anti-COX-1 variant antibodies of the invention can be used to detect and isolate COX-1 variant proteins, regulate the bioavailability of COX-1 variant proteins, and modulate COX-1 variant activity.

[00161] The invention provides a method (also referred to herein as a "screening assay") for identifying modulators, candidate or test compounds or agents peptides, peptidomimetics, small molecules or other drugs) which bind to COX-1 variant proteins COX-3, PCOX-la, PCOX-lb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs)), have a stimulatory or inhibitory effect on, for example, COX-1 variant expression or COX-1 variant activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of a COX-1 variant substrate. It is understood that the processes and methods for identifying screening) compounds for COX-1 variant modulating activity include manufacturing any compound so identified. Accordingly, the invention contemplates a method for making a compound that modulates the activity of a COX-1 variant by providing a cell transfected with a DNA encoding a COX-1 variant, wherein the cell expresses the variant; contacting said cell, in an intact or disrupted state, with a test compound; and determining whether the activity of the COX-1 variant is decreased or increased in the presence of the test compound, wherein a decrease or increase in said Cox-3 activity is an indication that the test compound modulates the activity of Cox-3 and manufacturing the compound so identified.

[00162 In one embodiment, the invention provides assays for screening candidate or test compounds which are substrates of COX-1 variant protein or polypeptide or biologically active portion thereof. In another embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of a COX-1 variant protein or polypeptide or biologically active portion thereof, modulate the ability of COX-1 variant to interact with its cognate ligand. The test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'onebead one-compound' library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K.S. (1997) Anticancer Drug Des. 12:145).

Combinatorial libraries are described in detail below.

WO 03/029411 PCT/US02/30947 [00163] In another embodiment, an assay is a cell-based assay comprising contacting a cell expressing a COX-1 variant target molecule arachadonic acid) with a test compound and determining the ability of the test compound to modulate stimulate or inhibit) the activity of the COX-1 variant target molecule. Determining the ability of the test compound to modulate the activity of a COX-1 variant on a target molecule can be accomplished, for example, by determining the ability of the COX-1 variant protein to bind to or interact with the compound target molecule, or by determining the ability of the COX-1 variant protein to modify the test molecule.

[00164] Determining the ability of the COX-1 variant protein to bind to or interact with a target molecule can be accomplished by determining direct binding. Determining the ability of the COX-1 variant protein to bind to or interact with a COX-1 variant target molecule can be accomplished, for example, by coupling the COX-1 variant protein with a radioisotope or enzymatic label such that binding of the COX-1 variant protein to a COX-1 variant target molecule can be determined by detecting the labeled COX-1 variant protein in a complex.

For example, COX-1 variant molecules, COX-1 variant proteins, can be labeled with 125, 35S, 1 4 C, or 3 H, either directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting. Alternatively, COX-1 variant molecules can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.

[00165] It is also within the scope of this invention to determine the ability of a compound to modulate the interaction between COX-1 variant and its target molecule, without the labeling of any of the interactants. For example, a microphysiometer can be used to detect the interaction of COX-1 variant with its target molecule without the labeling of a COX-1 variant or the target molecule. McConnell, H. M. et al. (1992) Science 257:1906-1912. As used herein, a "microphysiometer" Cytosensor) is an analytical instrument that measures the rate at which a cell acidifies its environment using a light-addressable potentiometric sensor (LAPS). Changes in this acidification rate can be used as an indicator of the interaction between compound and receptor.

[00166] In a preferred embodiment, determining the ability of the COX-1 variant protein to bind to or interact with a COX-1 variant target molecule can be accomplished by determining the activity of the target molecule. For example, the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target intracellular Ca 2 diacylglycerol, IP3, etc.), detecting catalytic/enzymatic activity 46 WO 03/029411 PCT/US02/30947 of the target an appropriate substrate, detecting the induction of a reporter gene (comprising a target-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, chloramphenicol acetyl transferase), or detecting a target-regulated cellular response.

[00167] One example of a simple in vitro system for the screening of compounds that modulate the activity of a COX-1 variant protein includes assays performed on living cells or on microsomal extracts prepared from the cultured cells. The COX-1 variant -synthesizing cell lines disclosed herein are useful for evaluating the activity of a compound on the activity of a COX-1 variant in comparison to the activity of the same compound on, for example, COX-1 or COX-2.

[00168] Thus, the present invention also provides a method to evaluate the relative inhibitory activity of a compound to selectively inhibit a COX-1 variant versus COX-1 or COX-2 activity, and thus to specifically inhibit the COX-1 variant activities associated with, for example, inflamed mammalian tissues, preferably human tissues, or in other physiological or pathological conditions in a mammalian host, preferably a human host. Such an assay can comprise contacting a COX-1 variant-expressing cell line or a microsomal extract thereof with a preselected amount of the compound in a suitable culture medium or buffer, adding a substrate arachidonic acid) to the mixture, and measuring the level of synthesis of a COX- 1 variant-mediated arachidonic acid metabolite, or the synthesis of any other metabolite unique to the cyclooxygenase pathway, by the cell line, or microsomal extract, as compared to a control cell line or portion of microsomal extract in the absence of said compound. The compound can be evaluated for its ability to selectively inhibit COX- 1 variants or COX- 1 or COX-2 by performing a second assay, in parallel, employing the above-described steps, with a COX-1 and/or COX-2 expressing cell line.

00169] In yet another embodiment, an assay of the present invention is a cell-free assay in which a COX-1 variant protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the COX-1 variant protein or biologically active portion thereof is determined. Binding of the test compound to the COX- 1 variant protein can be determined either directly or indirectly as described above. In a preferred embodiment, the assay includes contacting the COX-1 variant protein or biologically active portion thereof with a known compound which binds COX-1 variant to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with a COX-1 variant protein, wherein determining the ability of the test compound to interact with a COX-1 variant protein 47 WO 03/029411 PCT/US02/30947 comprises determining the ability of the test compound to preferentially bind to or biologically active portion thereof as compared to the known compound.

[00170] For example, the present studies have identified COX-1 variants that are inhibited by compounds that have little or no inhibitory activity against COX-1 or COX-2, including analgesic/antipyretic compounds such as acetaminophen, phenacetin, antipyrine and dipyrone (see Table 1, and Figure 13). The screening methods described herein provide the means by which derivatives of such compounds can be identified for their selective inhibition of COX- 1 variant activity. Such compounds are useful for treating a COX-1 variant-associated disorder in a subject. For example, acetaminophen is often categorized as a nonsteroidal antiinflammatory drug (NSAID) despite the fact that in clinical practice and in animal models it possesses little anti-inflammatory activity. Like NSAIDs, however, acetaminophen inhibits pain and fever. It has been shown that acetaminophen generally inhibits COX activity in dog brain homogenates more than in homogenates from spleen (Flower and Vane, (1972) Nature 240:410-411). However, as previous and current studies indicate, neither COX-1 nor COX-2 is inhibited by acetaminophen at physiological concentrations of the drug in whole cells or homogenates (Botting (2000) Clin. Infect. Dis. 31:8202-8210.) suggesting that neither isozyme is a good candidate for the site of action of acetaminophen. The present study indicates that COX-1 variants are clearly enriched in dog brain and the human 5.2kb transcript is highest in brain cortex. Further, epidemiologic evidence indicates that NSAID use is associated with a lower incidence or risk of Alzheimer's Disease An inverse relationship is seen between NSAID use (particularly aspirin), and AD incidence in casecontrolled studies of patients who have osteoarthritis, rheumatoid arthritis, or who use NSAIDs for other purposes. A similar inverse correlation was seen in a co-twin control study of 50 elderly twins with AD onset separated by 3 years or more. Both decreased risk of AD among NSAID users as well as an decreased risk of AD with increased duration of NSAID use was found in the prospective Baltimore Longitudinal Study of Aging and a decrease in cognitive decline was associated with NSAID use in the 1-year Rotterdam Study.

[00171] In another embodiment, the assay is a cell-free assay in which a COX-1 variant protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate stimulate or inhibit) the activity of the COX-1 variant protein or biologically active portion thereof is determined. Determining the ability of the test compound to modulate the activity of a COX-1 variant protein can be accomplished, for example, by determining the ability of the COX-1 variant protein to bind to a COX-1 variant target molecule by one of the methods described above for determining direct binding.

48 WO 03/029411 PCT/US02/30947 Determining the ability of the COX-1 variant protein to bind to a COX-1 variant target molecule can also be accomplished using a technology such as real-time Biomolecular Interaction Analysis (BIA). Sjolander, S. and Urbaniczky, C. (1991)Anal. Chem. 63:2338- 2345 and Szabo et al. (1995) Curr. Opin. Struct. Biol. 5:699-705. As used herein, "BIA" is a technology for studying biospecific interactions in real time, without labeling any of the interactants BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.

[00172] In yet another embodiment, the cell-free assay involves contacting a COX-1 variant protein or biologically active portion thereof with a known compound which binds the COX-1 variant protein to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the COX-1 variant protein, wherein determining the ability of the test compound to interact with the COX-1 variant protein comprises determining the ability of the protein to preferentially bind to or modulate the activity of a target molecule.

[00173] In more than one embodiment of the above assay methods of the present invention, it may be desirable to immobilize either COX-1 variant or its target molecule to facilitate separation of complexed from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of a test compound to a COX-1 variant protein, or interaction of a COX-1 variant protein with a target molecule in the presence and absence of a candidate compound, can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtitre plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix. For example, glutathione-S-transferase/ COX-1 variant fusion proteins or glutathione-S-transferase/target fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St.

Louis, MO) or glutathione derivatized microtitre plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or COX-1 variant protein, and the mixture incubated under conditions conducive to complex formation at physiological conditions for salt and pH). Following incubation, the beads or microtitre plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above. Alternatively, the complexes can be dissociated from the WO 03/029411 PCT/US02/30947 matrix, and the level of COX-1 variant binding or activity determined using standard techniques.

[00174] In another embodiment, modulators of COX-1 variant expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of COX- 1 variant mRNA or protein in the cell is determined. The level of expression of COX-1 variant mRNA or protein in the presence of the candidate compound is compared to the level of expression of COX-1 variant mRNA or protein in the absence of the candidate compound.

The candidate compound can then be identified as a modulator of COX-1 variant expression based on this comparison. For example, when expression of COX-1 variant mRNA or protein is greater (statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of COX-1 variant mRNA or protein expression. Alternatively, when expression of COX-1 variant mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of COX-1 variant mRNA or protein expression. The level of COX-1 variant mRNA or protein expression in the cells can be determined by methods described herein for detecting COX-1 variant mRNA or protein.

[00175] In another embodiment, the nucleic acid and polypeptide sequences disclosed herein provide a method for making structure-based predictions about the behavior of a COX-1 variant enzyme in the presence or absence of a test compound. Such in silico methods are based on mathematical algorithms that manipulate various types of structural information based in part on the primary amino acid structure of a polypeptide. Additional information generated from homologous or partially homologous proteins can be integrated into the method in order to augment the amino acid structure information. Thus, the polypeptide sequence information disclosed herein for novel COX-1 variant proteins can be used, in conjunction with structural information available from COX-1 and COX-2 studies, to predict which compounds, or family of compounds, will specifically interact with a COX-1 variant protein. The entire process can be accomplished in silico by algorithms known to those skilled in the art.

[00176] For example, substantial information regarding COX structural motifs and their effect on functional activity is available. COX-1 and COX-2 dimers are held together via molecular interactions involving the dimerization domains of each monomer.

Heterodimerization of COX-1 and COX-2 subunits does not occur. The dimerization domain is encoded by approximately 50 amino acids near the amino terminus of the proteolytically WO 03/029411 PCT/US02/30947 processsed protein. Three disulfide bonds hold this domain together in a structure reminiscent of epidermal growth factor (EGF). A fourth disulfide bond links the dimerization domain with the globular catalytic domain. The presence of disulfide bonds, which require an oxidizing environment to form, is consistent with the concept that COX-1 and COX-2 are located inside the lumen of the nuclear envelope, ER, or golgi, which have redox states that are significantly less reduced than cytosol.

[00177 COX isozymes associate with the intralumenal surface of microsomal membranes in an unusual fashion. Rather than employing transmembrane spanning sequences or covalently-bound lipids for attachment, COX isozymes contain a tandem series of four amphipathic helices which creates a hydrophobic surface that penetrates into the lumenal-side of the hydrophobic core of the lipid bilayer. These helices are encoded by approximately amino acids found immediately carboxyterminal to the bulk of the dimerization domain. The helices allow COX dimers to attach to the inside surface of the lumen of the ER/nuclear envelope, with the majority of the protein protruding into the lumenal space of these compartments. The membrane binding domain also forms the mouth of a narrow, hydrophobic channel that is the cyclooxygenase active site.

[00178] Carboxy-terminal to the membrane binding domain in COX primary structures is the catalytic domain, which comprises 80% (approximately 480 amino acids) of the protein and contains two distinct enzymatic active sites. The first is a peroxidase (POX) active site.

The entire catalytic domain of COX isozymcs is globular with 2 distinct intertwining lobes.

The interface of these lobes creates a shallow cleft on the upper surface of the enzyme (i.e.

the surface furthest from the membrane) where the peroxidase active site is located and where heme is bound. Coordination of the heme is via an iron-histidine bond involving His 388 in sheep COX-1. Other important interactions between the protoporphyrin also occur and specific amino acids which may function in coordinating PGG2 have been identified. The geometry of heme binding leaves a large portion of one side of the heme exposed in the open cleft of the peroxidase active site for interaction with PGG2 and other lipid peroxides.

[00179 The second distinct enzymatic active site in the catalytic domain is a cyclooxygenase (COX) active site. The cyclooxgyenase active site is a long, narrow, deadend channel of largely hydrophobic character whose entrance is framed by the four amphipathic helices of the membrane binding domain. The channel extends approximately angstroms into the globular catalytic domain and is on average about 8 angstroms wide.

However, significant narrowing of the channel is observed where arginine 120, one of only two ionic residues found in the COX active site, protrudes into the channel and forms a 51 WO 03/029411 PCT/US02/30947 hydrogen bonded network with glutamate 524 (the other ionic residue in the channel) and tyrosine 355. Arginine 120 is essential for substrate binding in COX-1 but appears to be significantly less important in COX-2. Arginine 120 is also clearly important in the binding of carboxylate-containing NSAIDs in the COX-1 active site but as with AA binding, it is significantly less important in coordinating these NSAIDs in COX-2.

[00180] The upper portion of the channel, or catalytic pocket, contains tyrosine 385 that forms a tyrosyl radical, abstracts hydrogen from the pro-S side of carbon 13 of AA, and creates an activated fatty acid radical that undergoes the cyclization and/or oxygenation reaction (see Figure Also in the hydrophobic pocket is Ser 530, which is transacetylated by aspirin. The hydroxyl of serine 530 itself is not essential for catalysis. However, its acetylation prevents abstraction of hydrogen from AA in COX-1 by sterically preventing AA from binding productively in the active site. In contrast, abstraction of hydrogen does occur in acetylated COX-2, but cyclization of the fatty acid radical and formation of the endoperoxide does not occur, yielding 15-R-hydroxyeicosotetraenoic acid rather than COX-2.

[00181] A structural difference between the active sites of COX-1 and COX-2 is a substitution ofisoleucine 523 in COX-1 for a valine in COX-2. This single difference opens a hydrophobic outpocketing in COX-2 that can be accessed by some COX-2 selective drugs.

There are other changes in residues that are near but do not line the COX active site, so-called second shell residues, that result in subtle changes and a slightly enlarged COX-2 active site relative to COX-1.

00182 As previously noted, NSAIDs are analgesic/antiinflammatory/antipyretic medications that act as inhibitors of the cyclooxygenase active site of COX isozymes.

Important mechanistic differences in the actions of individual NSAIDs with the COX active site exist. Of the NSAIDs in medical use, only aspirin is a covalent modifier of COX-1 and COX-2. The crystallographic studies of Garavito and colleagues demonstrated why this drug so efficiently acetylates serine 530 of COX-1 (Loll,1995, cite). Like other NSAIDs, aspirin diffuses into the COX active site of enzyme through the mouth of the channel and traverses up the channel to the constriction point formed by Arg 120, Tyr 355, and Glu 524. At this point in the channel, the carboxyl of aspirin forms a weak ionic bond with the side-chain of Arg 120. This positions aspirin only 5 angstroms below Ser 530 and in the correct orientation for transacetylation. Because the catalytic pocket of the channel is somewhat larger in COX-2 than in COX-1, orientation of aspirin for attack on Ser 530 is not as good in WO 03/029411 PCT/US02/30947 COX-2 and transacetylation efficiency is reduced. This accounts for the 10-100-fold lowered sensitivity to aspirin of COX-2 in comparison to COX-1.

[00183] Other NSAIDs in addition to aspirin inhibit COX-1 and COX-2 by competing with AA for binding in the COX active site. However, NSAIDs significantly differ from each other in whether they bind the COX active site in a time-dependent or independent fashion.

For example, NSAIDs differ dramatically with regard to how quickly they productively bind in the COX active site and how quickly they come out of the COX channel. Some NSAIDs, such as ibuprofen, have very rapid on and off rates. They inhibit COX activity essentially instantaneously after addition of the NSAID and they readily wash out of the COX active site when the NSAID is removed from the environment of the enzyme. In contrast, many NSAIDs such as indomethacin and diclofenac are time-dependent. They require typically seconds to minutes to bind the COX active site. Once bound, however, these drugs typically have low off-rates that may require many hours for the NSAID to wash out of the active site.

Time-dependent NSAIDs compete very poorly with AA in instantaneous assays of COX activity. Co-crystallization studies have been performed for flurbiprofen and COX-1 and COX-2 as well as indomethacin and COX-1 which define the precise binding interactions of carboxyl-containing NSAIDs in the COX binding site.

[00184] NS398 is a particularly important COX-2 inhibitor which is commercially available and, therefore, is widely used in pharmacology studies. Celecoxib, rofecoxib, and NS398 have been co-crystallized with COX-2. Celecoxib and rofecoxib are diaryl compounds containing a sulfonamide and methylsulfone, respectively, rather than a carboxyl group. Hence, the identification of COX isozymes has allowed the eventual synthesis and testing of NSAIDs, in the form of celecoxib, rofecoxib, that have resulted in important therapeutic agents.

[00185] By combining the structural information available for COX-1 and COX-2 with the novel sequence information for COX-1 variants disclosed herein and the compound inhibition studies disclosed herein, one skilled in the art can predict the three-dimensional structure of a COX-1 variant and subsequently select potential inhibitors of a COX-1 variant.

Accordingly, the invention encompasses a method for identifying a potential inhibitor for a COX-1 variant by providing a three-dimensional structure of the COX-1 variant as defined by atomic coordinates and employing the three-dimensional structure to design or select a potential inhibitor. The method further involves synthesizing the potential inhibitor and contacting the potential inhibitor with the COX-1 variant in the presence or absence of a WO 03/029411 PCT/US02/30947 substrate of COX-1 variant to determine the ability of the potential inhibitor to inhibit enzyme Z.

0 018 6] The invention fiurther provides a method for identifying a potential inhibitor of a COX-1 variant by providing the three-dimensional coordinates of an inhibitor when it is bound to COX-1 variant and comparing the three-dimensional coordinates of the inhibitor when it is bound to the COX-1 variant to the three-dimensional coordinates of compounds in a database of compound structures and selecting from the database at least one compound that is structurally similar to the inhibitor when it is bound to the COX-1 variant.

0 0187] The invention further provides a method for identifying a potential inhibitor of a COX-1 variant by providing the three-dimensional coordinates and identities of the atoms of inhibitor I when it is bound to the COX- 1 variant; selecting a subset of atoms of the inhibitor that govern its interaction with the COX-1 variant; comparing the three-dimensional coordinates of the selected subset of atoms of the inhibitor with the three-dimensional coordinates of compounds in a database of compound structures; and selecting from the database at least one compound comprising three-dimensional coordinates that are identical to the three-dimensional coordinates of the selected subset of atoms of inhibitor, wherein the selected compound is a potential inhibitor of a COX-1 variant.

[00188] In another embodiment, the novel polypeptides of the invention can be expressed and crystallized in the presence of absence of a test compound. Once crystallized, the threedimensional structure of a COX-1 variant polypeptide may be determined in a number of ways. Many of the most precise methods employ X-ray crystallography (for a general review, see, Van Holde, Physical Biochemistry, Prentice-Hall, N. J. pp. 221-239, (1971), which is incorporated herein by reference). This technique relies on the ability of crystalline lattices to diffract X-rays or other forms of radiation. Diffraction experiments suitable for determining the three-dimensional structure ofmacromolecules typically require high-quality crystals. Various methods for preparing crystalline proteins and polypeptides are known in the art (see, for example, McPherson, et al. "Preparation and Analysis of Protein Crystals", A.

McPherson, Robert E. Krieger Publishing Company, Malabar, Fla. (1989); Weber, Advances in Protein Chemistry 41:1-36 (1991); U.S. Pat. No. 4,672,108; and U.S. Pat. No. 4,833,233; all of which are incorporated herein by reference for all purposes).

[00189] This invention further pertains to novel agents or compounds identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an compound identified as described herein in an appropriate animal model. For example, an compound identified as described herein a COX-1 variant modulating 54 WO 03/029411 PCT/US02/30947 compound, an antisense COX-1 variant nucleic acid molecule, a COX-1 variant -specific antibody, or a COX-1 variant -binding partner) can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an compound. Alternatively, an compound identified as described herein can be used in an animal model to determine the mechanism of action of such an compound. Furthermore, this invention pertains to uses of novel compounds identified by the above-described screening assays for treatments as described herein.

[00190] The invention further contemplates the use of high-throughput screening techniques to identify candidate compounds that modulate the activity of COX-1 variants of the invention. Conventionally, new chemical entities with useful properties are generated by identifying a chemical compound (called a "lead compound") with some desirable property or activity, creating variants of the lead compound, and evaluating the property and activity of those variant compounds. However, the current trend is to shorten the time scale for all aspects of drug discovery. Because of the ability to test large numbers quickly and efficiently, high throughput screening (HTS) methods are replacing conventional lead compound identification methods.

[001911 In one preferred embodiment, high throughput screening methods involve providing a library containing a large number of potential therapeutic compounds (candidate compounds). Such "combinatorial chemical libraries" are then screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds" or can themselves be used as potential or actual therapeutics.

0 0 192 Combinatorial chemical libraries are a preferred means to assist in the generation of new chemical compound leads. A combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical "building blocks" such as reagents. For example, a linear combinatorial chemical library such as a polypeptide library is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length the number of amino acids in a polypeptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks. For example, one commentator has observed that the systematic, combinatorial mixing of 100 interchangeable chemical building blocks results in the theoretical synthesis of WO 03/029411 PCT/US02/30947 100 million tetrameric compounds or 10 billion pentameric compounds (Gallop et al. (1994) 37(9): 1233-1250).

[00193 Preparation and screening of combinatorial chemical libraries are well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, U.S. Patent 5,010,175, Furka (1991) Int. J. Pept. Prot. Res., 37: 487-493, Houghton et al. (1991) Nature, 354: 84-88). Peptide synthesis is by no means the only approach envisioned and intended for use with the present invention. Other chemistries for generating chemical diversity libraries can also be used. Such chemistries include, but are not limited to: peptoids (PCT Publication No WO 91/19735, 26 Dec. 1991), encoded peptides (PCT Publication WO 93/20242, 14 Oct. 1993), random bio-oligomers (PCT Publication WO 92/00091, 9 Jan. 1992), benzodiazepines Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., (1993) Proc. Nat. Acad. Sci. USA 6909-6913), vinylogous polypeptides (Hagihara et al. (1992) J. Amer. Chem. Soc. 114: 6568), nonpeptidal peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann et al., (1992) J. Amer. Chem. Soc. 114: 9217-9218), analogous organic syntheses of small compound libraries (Chen et al. (1994) J. Amer. Chem. Soc. 116: 2661), oligocarbamates (Cho, et al., (1993) Science 261:1303), and/or peptidyl phosphonates (Campbell et al., (1994) J. Org. Chem. 59: 658). See, generally, Gordon et al., (1994) J. Med. Chem. 37:1385, nucleic acid libraries, peptide nucleic acid libraries (see, U.S. Patent 5,539,083) antibody libraries (see, Vaughn ct al. (1996) Nature Biotechnology, 14(3): 309-314), and PCT/US96/10287), carbohydrate libraries (see, Liang et al. (1996) Science, 274: 1520- 1522, and U.S. Patent 5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Baum (1993) C&EN, Jan 18, page 33, isoprenoids U.S. Patent 5,569,588, thiazolidinones and metathiazanones U.S. Patent 5,549,974, pyrrolidines U.S. Patents 5,525,735 and 5,519,134, morpholino compounds U.S. Patent 5,506,337, benzodiazepines 5,288,514, and the like).

[00194] Devices for the preparation of combinatorial libraries are commercially available (see, 357 MPS, 390 MPS, Advanced Chem Tech, Louisville KY, Symphony, Rainin, Woburn, MA, 433AApplied Biosystems, Foster City, CA, 9050 Plus, Millipore, Bedford, MA). A number of well known robotic systems have also been developed for solution phase chemistries. These systems include automated workstations like the automated synthesis apparatus developed by Takeda Chemical Industries, LTD. (Osaka, Japan) and many robotic systems utilizing robotic arms (Zymate II, Zymark Corporation, Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto, Calif.) which mimic the manual synthetic operations performed 56 WO 03/029411 PCT/US02/30947 by a chemist. Any of the above devices are suitable for use with the present invention. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art. In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, Asinex, Moscow, Ru, Tripos, Inc., St. Louis, MO, ChemStar, Ltd, Moscow, RU, 3D Pharmaceuticals, Exton, PA, Martek Biosciences, Columbia, MD, etc.).

[00195] Any of the assays for compounds capable of modulating COX-1 variant activity described herein are amenable to high throughput screening. High throughput screening systems are commercially available (see, Zymark Corp., Hopkinton, MA; Air Technical Industries, Mentor, OH; Beckman Instruments, Inc. Fullerton, CA; Precision Systems, Inc., Natick, MA, etc.). These systems typically automate entire procedures including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. The manufacturers of such systems provide detailed protocols the various high throughput. Thus, for example, Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like.

[00196] Portions or fragments of the novel cDNA sequences identified herein can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample.

[00197] Monitoring the influence of agents drugs or compounds) on the expression or activity of a COX-1 variant protein can be applied not only in basic drug screening, but also in clinical trials. For example, the effectiveness of an agent determined by a screening assay as described herein to increase COX-1 variant gene expression, protein levels, or upregulate COX-1 variant activity, can be monitored in clinical trials of subjects exhibiting decreased COX-1 variant transcript expression, protein levels, or downregulated COX-1 variant activity. Alternatively, the effectiveness of an agent determined by a screening assay to decrease COX-1 variant gene expression, protein levels, or downregulate COX-1 variant activity, can be monitored in clinical trials of subjects exhibiting increased COX-1 variant gene expression, protein levels, or upregulated COX-1 variant activity. In such clinical trials, WO 03/029411 PCT/US02/30947 the expression or activity of a gene, and preferably, other genes that have been implicated in a disorder can be used as a "read out" or markers of the phenotype of a particular cell.

[00198] In a preferred embodiment, the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) comprising the steps of (i) obtaining a pre-administration sample from a subject prior to administration of the agent; (ii) detecting the level of expression of a COX-1 variant protein, mRNA in the pre-administration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the protein or mRNA in the postadministration samples; comparing the level of expression or activity of the protein or mRNA in the pre-administration sample with the protein or mRNA in the post administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly.

For example, increased administration of the agent may be desirable to increase the expression or activity of a COX-1 variant to higher levels than detected, to increase the effectiveness of the agent. Alternatively, decreased administration of the agent may be desirable to decrease expression or activity of COX-1 variant to lower levels than detected, i.e. to decrease the effectiveness of the agent. According to such an embodiment, COX-1 variant expression or activity may be used as an indicator of the effectiveness of an agent, even in the absence of an observable phenotypic response.

00199] The present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant COX-1 variant expression or activity. With regards to both prophylactic and therapeutic methods of treatment, such treatments may be specifically tailored or modified, based on knowledge obtained from the field ofpharmacogenomics. "Pharmacogenomics", as used herein, refers to the application of genomics technologies such as gene sequencing, statistical genetics, and gene expression analysis to drugs in clinical development and on the market. More specifically, the term refers the study of how a patient's genes determine his or her response to a drug a patient's "drug response phenotype", or "drug response genotype".) Thus, another aspect of the invention provides methods for tailoring an individual's prophylactic or therapeutic treatment with either the COX-1 variant molecules of the present invention or modulators according to that individual's drug response genotype.

Pharmacogenomics allows a clinician or physician to target prophylactic or therapeutic WO 03/029411 PCT/US02/30947 treatments to patients who will most benefit from the treatment and to avoid treatment of patients who will experience toxic drug-related side effects.

[00200] Accordingly, the present invention also provides diagnostic assays for identifying the presence or absence of a genetic alteration characterized by at least one of(i) aberrant modification or mutation of a gene encoding a COX-1 variant protein; (ii) mis-regulation of the gene; and (iii) aberrant post-translational modification of a COX-1 variant protein, wherein a wild-type form of the gene encodes a protein with a COX-1 variant activity. The invention further provides diagnostic assays for determining the relative expression levels of a COX-1 variant transcript or polypeptide in relation to a COX-1 or COX-2 transcript or polypeptide. A diagnostic assay can include, for example, an array-based system for detecting the presence or absence of a COX-1 variant or the presence or absence of a genetic alteration in a COX-1 variant. An array-based system can include a) bead arrays, bead based arrays, bioarrays, bioelectronic arrays, cDNA arrays, cell arrays, DNA arrays, encoded bead arrays, gel pad arrays, gene arrays, gene expression arrays, genome arrays, genomic arrays, high density oligonucleotide arrays, high density protein arrays, hybridization arrays, in situ arrays, low density arrays, microelectronic arrays, multiplex DNA hybridization arrays, nanoarrays, nylon macroarrays, oligo arrays, oligonucleotide arrays, oligosaccharide arrays, peptide arrays, planar arrays, protein arrays, solution arrays, spotted arrays, tissue arrays, exon arrays, filter arrays, macroarrays, small molecule microarrays, suspension arrays, theme arrays, tiling arrays or transcript arrays that incorporate.

[00201] For example, an array comprising a nucleic acid, protein or polypeptide of the invention or molecule that interacts with a nucleic acid, protein or polypeptide of the invention can be used in detection assays, diagnostic assays and in assays for monitoring the effects of a compound during clinical trials. Accordingly, such an array can include a nucleic acid, protein or polypeptide of the invention or molecule that interacts with a nucleic acid, protein or polypeptide disclosed herein, including COX-3, PCOX-la, PCOXlb, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs).

[00202] In one aspect, the invention provides a method for preventing, in a subject, a disease or condition associated with an aberrant COX-1 variant expression or activity, by administering to the subject a COX-1 variant or a compound which modulates COX-1 variant expression or at least one COX-1 variant activity. Subjects at risk for a disease which is caused or contributed to by aberrant COX-1 variant expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein.

Administration of a prophylactic agent can occur prior to the manifestation of symptoms 59 WO 03/029411 PCT/US02/30947 characteristic of the COX-1 variant aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression. Depending on the type of COX-1 variant aberrancy, for example, a COX-1 variant, agonist or antagonist agent can be used for treating the subject. The appropriate agent can be determined based on screening assays described herein.

[00203] Accordingly, the invention provides a method of selecting a therapy for a patient by providing a subject expression profile of a sample from said patient; providing a plurality of reference profiles, each associated with a therapy, wherein the subject expression profile and each reference profile has a plurality of values, each value representing the expression level of a COX- 1 variant transcript or polypeptide; and selecting the reference profile most similar to the subject expression profile, to thereby select a therapy for said patient.

[00204] The invention further provides an array comprising a substrate having a plurality of addresses, wherein each address has disposed thereon a capture probe that can specifically bind a COX-1 variant nucleic acid. The nucleic acids can be selected from the group consisting of COX-1 variant SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12 or SEQ ID NO:13. The substrate can possess a range of addresses, each corresponding to a unique COX-1 variant sequence. The range of addresses can include 5 10,000, depending on the density of the array.

[00205] The invention further provides a method of choosing a therapy for a patient, by providing a plurality of reference expression profiles, each associated with a therapy; providing a nucleic acid obtained from a patient; contacting the nucleic acid with the array comprising a substrate having a plurality of addresses, wherein each address has disposed thereon a capture probe that can specifically bind a COX- 1 variant nucleic acid; detecting binding of the nucleic acid to each address of the plurality of addresses to thereby provide a subject expression profile; and selecting the reference profile most similar to the subject expression profile, to thereby choose a therapy for said patient.

[00206] The invention further provides a method for evaluating whether or not a pharmaceutical composition will be effective for interacting with a COX-1 variant. The method can utilize an array having a substrate including a plurality of addresses, wherein each address has disposed thereon a capture probe that can specifically bind a COX-1 variant nucleic acid; and a computer-readable medium having a plurality of digitally-encoded expression profiles wherein each profile of the plurality has a plurality of values, each value representing the expression of a COX-1 variant nucleic acid detected by the array.

WO 03/029411 PCT/US02/30947 [00207] The invention further encompasses a method of selecting a therapy for a subject by obtaining a subject sample from a caregiver; obtaining a nucleic acid from the subject sample; identifying a subject expression profile from the nucleic acid; selecting from a plurality of reference profiles a matching reference profile most similar to the subject expression profile, wherein the reference profiles and the subject expression profile have a plurality of values, each value representing the expression level of a COX-1 variant, wherein each reference profile of the plurality of reference profiles is associated with a therapy; and transmitting a descriptor of the therapy associated with the matching reference profile to the caregiver, thereby selecting a therapy for said subject.

[00208] The invention further provides a kit for evaluating a pharmaceutical composition, the kit comprising an array as described above and a computer-readable medium having a plurality of expression profiles, wherein each profile of the plurality has a plurality of values, each value representing the expression of a COX-1 variant nucleic acid detected by the array.

[002091 Another aspect of the invention pertains to methods of modulating COX- 1 variant expression or activity for therapeutic purposes. Accordingly, in an exemplary embodiment, the modulatory method of the invention involves contacting a cell with a COX-1 variant or agent that modulates one or more of the activities of COX-1 variant protein activity associated with the cell. A compound or agent that modulates COX-1 variant protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring target molecule of a COX-1 variant protein, a COX-1 variant antibody, a COX-1 variant agonist or antagonist, a peptidomimetic of a COX-1 variant agonist or antagonist, or other small molecule. In one embodiment, the agent stimulates one or more COX-1 variant activities. Examples of such stimulatory agents include active COX-1 variant protein and a nucleic acid molecule encoding COX-1 variant that has been introduced into the cell. In another embodiment, the agent inhibits one or more COX-1 variant activites. Examples of such inhibitory compounds or agents include antisense COX-1 variant nucleic acid molecules, anti-COX-1 variant antibodies, and COX-1 variant inhibitors. These modulatory methods can be performed in vitro by culturing the cell with the agent) or, alternatively, in vivo by administering the agent to a subject) or even in silico, as described elsewhere.

As such, the present invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant expression or activity of COX-1 variant protein or nucleic acid molecule.

[00210] The COX-1 variant nucleic acid molecules, COX- 1 variant proteins, compounds identified as modulating a COX-1 variant activity and anti- COX-1 variant antibodies (also 61 WO 03/029411 PCT/US02/30947 referred to herein as "active compounds") of the invention can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically comprise the nucleic acid molecule, protein, compound or antibody and a pharmaceutically acceptable carrier. As used herein the language "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated.

Supplementary active compounds can also be incorporated into the compositions.

[00211] For example, epidemiologic and clinical data suggest that the use non-steroidal anti-inflammatory drugs (NSAIDs) delays the onset of AD and reduces the progression of pathologic symptoms in Alzheimer's disease. McGeer and McGeer, Brain Res. Rev. 21, 195 (1995). Aspirin, like most NSAIDs, prevent inflammation and pain by inhibiting both COX-1 and COX-2 enzymes. Resveratrol, a phenolic antioxidant and COX inhibitor found in grapes, inhibits prostaglandin production, and has anti-cancer and anti-inflammatory properties. Jang et al., Science 275, 218 (1997). Alzheimer's Disease (AD) is the most common neurodegenerative disorder of aging, and is characterized by progressive dementia and personality dysfunction. The abnormal accumulation of amyloid plaques in the vicinity of degenerating neurons and reactive astrocytes is a pathological characteristic of AD. The present invention further relates to compositions and methods for the treatment of various neurological diseases and neurodegenerative disorders. For example, a composition that modulates a COX-1 variant of the invention can be used to treat neurodegenerative diseases associated with an overabundance of Amyloid Precursor Protein (APP). Cytosolic phospholipase A2, which releases arachidonic acid from cellular phospholipids, is elevated in AD brain and after transient global ischemia. The cyclooxygenation of arachidonic acid, catalyzed by two forms ofcyclooxygenase (COX), COX-1 and COX-2, produces prostaglandins which, in turn, regulate neurotransmission, immune and inflammatory responses by activating receptors coupled to cAMP formation. cAMP elevations caused by activation of neurotransmitter receptors increased APP mRNA and holoprotein production in astrocytes.

[00212] Accordingly, active compounds identified by a screening assay disclosed herein can be in included in a pharmaceutical composition in order to ameliorate a COX-1 variant associated disorder such as, for example, a neurodegenerative condition or disease. The 62 WO 03/029411 PCT/US02/30947 condition can be treated in a subject by administering a specific inhibitor of COX-1 variant activity as disclosed in the invention, in a pharmaceutically acceptable carrier. It is further object of the invention to provide a method for preventing or treating Alzheimer's Disease in a subject by administering an effective amount of a specific inhibitor of COX-1 variant activity as disclosed in the present invention.

[00213] The invention further provides a method for treating immune or inflammatory conditions associated with a neurodegenerative condition in a subject by administering a specific inhibitor of a COX-1 variant as provided in the this disclosure. The invention encompasses a method of modulating expression, production, or formation of amyloid precursor protein (APP) in a subject by administering an effective amount of an antagonist of a COX-1 variant of the invention. The antagonist can be, for example, a non-steroidal antiinflammatory agent that is a specific inhibitor of COX-1 variant activity, in a phannaceutically acceptable carrier. Thus, the present invention provides methods and compositions that can modulate or regulate the production or formation of APP in patients, including the expression of APP gene products and the transcription or translation of the APP gene in central nervous system. For example, the production of APP by mammalian cells, in particular, by cells in the brain, can be increased or reduced. In attaining this objective, it is also an objective of the invention to inhibit excessive amyloid formation, prevent neurite dystrophy and alleviate pathological symptoms, such as neurodegeneration or cognitive deficits that may arise from the negative effects of inappropriately expressed, produced, or formed amounts of APP.

[00214] Accordingly, the present invention is useful in the treatment or alleviation of disease, especially those disorders related to neurological diseases or neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, Lou Gehrig's disease, or multiple sclerosis, to name a few, not to mention central or peripheral nervous system damage, dysfunction, or complications involving same stemming from edema, injury, or trauma. Such damage, dysfunction, or complications may be characterized by an apparent neurological, neurodegenerative, physiological, psychological, or behavioral aberrations, the symptoms of which can be reduced by the administration of an effective amount of the active compounds or substances of the present invention.

00215 According to one embodiment, the administration of effective amounts of a composition that modulates the activity of a COX-1 variant of the invention can be used to suppress, inhibit, or neutralize the action of increased cAMP activity, which activity if unchecked leads to the overproduction of APP. A variety of non-steroidal anti-inflammatory 63 WO 03/029411 PCT/US02/30947 agents (NSAIDs) are found to be suitable for reversing the stimulatory effects of cAMP, its derivatives, a ligand, an agonist, or an antagonist of a receptor that is coupled to the cellular levels of cAMP, or a compound that enhances the nuclear actions of cAMP. Examples of suitable NSAIDs include, but are not limited to, Advil, Aspirin, Aleve, Anaprox, Diclofenac, Docosahexaenoic acid, Dolobid, Etodolac, Feldene, Flurbiprofen, Ibuprofen, Indomethacin, Ketorolac tromethamine, Lodine, Meclofenamate, 6-MNA, Motrin, Nalfon, Naprosyn, Nuprin, Orudis, Phenylbutazone, Piroxicam, Phenylbutazone, Ponstel, Relafen, Salicylic acid, Sulindac sulfide, Tolectin, Toradol, Voltaren; also 5-lipoxygenase inhibitors, phosphodiesterase inhibitors, or cyclooxygenase inhibitors cyclosalicylazosulfapyridine, azulfasalazine, DFU (5,5-dimethyl-3-(3-fluorophenyl)-4-(4or DFP (5,5-dimethyl-3-isopropyloxy-4-(4'- [0 02161 As used herein, the term "central nervous system" refers to all structures within the dura mater. Such structures include, but are not limited to, the brain and spinal cord.

[00217] As used herein, the terms "subject suffering from Alzheimer's disease," "subject suffering from a disease with an inflammatory component," and "subject suffering from central nervous system injury," refer to subjects that are identified as having or likely having the particular disease, injury, or condition, respectively. As used herein the terms "subject susceptible to Alzheimer's disease" and "subject susceptible to a disease with an inflammatory component," refer to subjects identified as having a risk of contracting or developing the particular disease, injury, or condition, respectively. As used herein, the term "disease with an inflammatory component" refers to diseases and conditions that are associated with an inflammatory element. The inflammatory element can comprise a symptom, side-effect, or causative event associated with the disease or condition. Diseases with an inflammatory component include, but are not limited to, stroke, ischemic damage to the nervous system, neural trauma percussive brain damage, spinal cord injury, and traumatic damage to the nervous system), multiple sclerosis and other immune-mediated neuropathies Guillain-Barre syndrome and its variants, acute motor axonal neuropathy, acute inflammatory demyelinating polyneuropathy, and Fisher Syndrome), HIV/AIDs dementia complex, and bacterial and viral meningitis. Such diseases further include degenerative diseases, such as Alzheimer's Disease Parkinson's Disease (PD), Amyotrophic lateral sclerosis (ALS), Huntington's Disease Pick's disease, progressive supranuclear palsy, striatonigral degeneration, cortico-basal degeneration, olivopontocerebellar atrophy, Leigh's disease, infantile necrotizing encephalomyelopathy, 64 WO 03/029411 PCT/US02/30947 Hunter's disease, mucopolysaccharidosis, various leukodystrophies (such as Krabbe's disease, Pelizaeus-Merzbacher disease and the like), amaurotic (familial) idiocy, Kuf's disease, Spielmayer-Vogt disease, Tay Sachs disease, Batten disease, Jansky- Bielschowsky disease, Reye's disease, cerebral ataxia, chronic alcoholism, beriberi, Hallervorden-Spatz; syndrome, cerebellar degeneration, and the like.

[00218] As used herein, the term "neurological defect" refers to a defect involving or relating to the nervous system. Some neurological defects are caused by defective tissues or cells of the nervous system, while other defects are caused by defective tissues or cells that affect the nervous system. As used herein, the term "neurologically defective mammal" refers to a mammal having one or more neurological defects. When a neurological defect is "ameliorated," the condition of the host is improved. For example, amelioration can occur when defective tissue is returned partially or entirely to a normal state. However, amelioration can also occur when tissue remains subnormal, but is otherwise altered to benefit the host. As used herein, the term "lesion" refers to a wound or injury, or to a pathologic change in a tissue.

[00219] A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, intravenous, intradermal, subcutaneous, oral inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

[00220] Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under WO 03/029411 PCT/US02/30947 the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.

[00221] Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

[00222] Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as WO 03/029411 PCT/US02/30947 colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.

[00223] For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.

[00224 Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.

[00225] The compounds can also be prepared in the form of suppositories with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.

[00226] In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811.

[00227] It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.

The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic WO 03/029411 PCT/US02/30947 effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.

00228 Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50.

Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.

[00229] The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

[00230 The nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Patent 5,328,470) or by stereotactic injection (see Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91:3054-3057). The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.

[00231] The invention also encompasses pharmaceutical compositions comprising a compound identified by a method of the invention contained in a container and labeled with instructions for use as a COX-lvariant specific inhibitor. The pharmaceutical composition 68 WO 03/029411 PCT/US02/30947 con be included in a kit with instructions for use of the composition in the treatment of a COX-1 variant associated disorder. The kit can further comprise instructions for using dosage. Accordingly, the invention contemplates an article of manufacture comprising packaging material and, contained within the packaging material, a compound that modulates the activity of a COX-1 variant, such as, for example, Cox-3, wherein the packaging material comprises a label or package insert indicating that said compound modulates the activity of a COX-1 variant and can be used for treating (pain/inflammation) in a subject. The invention further contemplates an article of manufacture comprising packaging material and, contained within the packaging material, a compound that preferentially modulates the activity of a COX-1 variant in comparison to Cox-1 and Cox-2, wherein the packaging material comprises a label or package insert indicating that said compound modulates the activity of a COX-1 variant and can be used for treating (pain/inflammation) in a subject.

Examples [00232] Recent studies have demonstrated that COX-1 possesses at least three distinct domains responsible for dimerization, membrane binding, and catalysis. A fourth domain, the N-terminal signal peptide, which is clearly evident in the primary structure of COX-1, was not observed because this sequence typically is co-translationally cleaved from the nascent polypeptide by microsomal signal peptidase. The amino terminal signal peptide directs synthesis of the COX isozymes into the lumen of the endoplasmic reticulum/nuclear envelope. Although cleaved from the nascent polypeptide, the amino terminal hydrophobic signal peptide shows a size difference between COX-1 and COX-2 that, prior to the present invention, had unknown biological significance. The signal peptide for COX-1 is generally 22-29 amino acids in length with a large hydrophobic core comprised of 4 or more leucines or isoleucines. This sequence is encoded by exons 1 and 2 of the COX-1 gene. Exon 2 of COX-1 terminates precisely at the cleavage site for the signal peptide. In contrast to COX-1, COX-2's signal peptide is 17 amino acids long in all species and it is encoded entirely by exon 1 of the COX-2 gene, which terminates precisely at the cleavage site for the signal peptide. Therefore, the hydrophobic signal peptide is precisely encoded by exons 1 and 2 in COX-1 and exon 1, alone, in the COX-2 gene. Intron 1 of the COX-1 gene is missing in the COX-2 gene. This represents a major difference in structure between the COX-1 and COX-2 genes.

[00233] In vitro translation experiments have demonstrated that COX-1 is rapidly translocated into the lumen of canine pancreatic microsomes, whereas COX-2 is inefficiently 69 WO 03/029411 PCT/US02/30947 translocated (Xie, et al. (1991) Proc. Natl. Acad. Sci. USA 88:2692-2696.). To date this is the only known biochemical property of the COX-1 and COX-2 isozymes to be affected by this difference in the length of the signal peptide. However, the discovery described herein shows that regulation of this important signal sequence by intron retention in COX-1 occurs in brain and other tissues to create unique variants COX-1 variants) of COX isozymes.

[00234] Accordingly, novel mRNAs encoding COX-variant proteins COX-3, PCOXla, hCOX-3(cc), hCOX-3(af), hCOX-3 (dellO) and hCOX-3(cs)) are expressed in mammalian tissue and are provided herein. For example, canine and human cerebral cortex express COX-1 variant mRNA. In addition, human COX-3 mRNA(~5.2 kb transcript) has been identified from heart tissue. Intron 1 is conserved in length and in sequence in mammalian COX-1 genes. This intron contains an open reading frame that introduces an insertion of 30-34 amino acids, depending on the mammalian species, into the hydrophobic signal peptide that directs COX-1 into the lumen of the endoplasmic reticulum and nuclear envelope. Also provided in the present invention are COX-variant proteins expressed efficiently in insect cells as membrane-bound proteins. COX-3 and PCOX-la are examples of COX-1 variants described herein. While the expression and activities of COX-3 and PCOX-la are specifically described, it is noted that such expression is applicable to any of the COX-1 variants provided in the disclosure. Accordingly, expression ofPCOXlb, hCOX- 3(cc), hCOX-3(af), hCOX-3 (dellO) or hCOX-3(cs) can be easily accomplished by the techniques described herein and by the knowledge of one skilled in the art of molecular biology.

[00235] Exemplary COX-3, but not PCOX-la, possesses cyclooxygenase activity and this activity is dependent on the enzyme being glycosylated. Methods of screening for compounds that selectively inhibit COX-1 variants are also provided. For example, COX-1 variant activity can be inhibited by analgesic/antipyretic drugs such as acetaminophen, phenacetin, antipyrine, dipyrone and NSAIDs. Therefore, methods for identifying compounds useful for treating, for example, central nervous system disorders decrease pain and/or fever) are provided.

[002 3 6] By way of example only, but not by way of limitation, the invention provides specific compounds that target a COX-1 variant for inhibition. Methods of manufacturing derivatives of such compounds are well known to those skilled in the art of biochemistry.

Thus, the invention encompasses derivatives of the disclosed compounds that are identified as possessing COX-1 variant inhibitory activity. Examples of COX inhibitors include Celecoxib (Celebrex®) and rofecoxib (Vioxx which were developed as COX-2 selective WO 03/029411 PCT/US02/30947 inhibitors. Other NSAIDs including meloxicam (Mobic®), nimesulide, and etodolac (Lodine were also identified COX-2 preferential inhibitors. The invention provides a mechanism for identifying variants of the above-described compounds that preferentially inhibit a COX-1 variant over that of COX-1 and or COX-2.

[00237] Analysis by Northern blot of COX mRNAs isolated from a variety of canine tissues demonstrated that all RNA samples, with the exception of those from brain (cortex), contained primarily a single 2.6 kb mRNA that hybridized to a canine COX-1 cDNA probe.

The canine probe was -1.Okbp in size and was made to the coding region of the COX-1 mRNA. This probe used in these experiments was generated by reverse transcriptioncoupled polymerase chain reaction (RT-PCR) using degenerate oligonucleotides made to conserved sequences in COX isozymes. The identity of the probe was confirmed by DNA sequencing. In contrast to what was observed in other tissues, this probe detected a novel COX-1 mRNA in total RNA isolated from brain tissue (Figure 5, panel This novel RNA was approximately 1.9 kb in size in contrast to the 2.6 kb mRNA that encodes COX-1 in dogs. A similarly sized message was detected in chicken brain mRNA (Figure 5, panel b).

[00238] Further Northern blot experimentation showed that the 1.9 kb mRNA was enriched in the poly A fraction of RNA and, therefore, was not likely a breakdown product of unprocessed RNA transcripts (Figure 5 panel Moreover, (RT-PCR) experiments demonstrated that this novel 1.9 kb COX-1-related mRNA was not the product of an alternative polyadenylation process which would change the length of the 3' untranslated region of the COX-1 RNA but otherwise leave the coding region unchanged. This was confirmed by Southern blot analysis ofPCR generated fragment using probes specific for the 3' untranslated region of the message. In these experiment the same 3' untranslated region was found to be be present in both the 2.0 and 2.8 kb COX-1 RNAs. Therefore, the 1.9 kb RNA appeared to reflect changes in the coding region of a COX-1 mRNA or in a highly related mRNA.

[00239] To identify changes in the coding region present in the 1.9 kb RNA, cDNA libraries were created in both lambda ZIPLOX® and lambda ZAP® cloning vectors purchased from Gibco BRL and Stratagene, respectively. Methods of cDNA synthesis, vector ligation, and phage propagation are known to those skilled in the art. Approximately 45,000 recombinants from the ZIPLOX® library and -149,000 recombinants from the lambdaZAP® libraries were probed with the canine 1.0 kb COX-1 cDNA fragment, radiolabeled with a32PCTP and hybridized at a concentration of 2 X 10 6 cpm/ml.

WO 03/029411 PCT/US02/30947 [00240] Eleven clones were isolated that strongly hybridized to the canine COX-1 clone and were subjected to DNA sequencing by automated DNA sequencing. All of these clones contained some DNA sequence that was essentially identical with canine COX-1 cDNA.

However, three clones contained an insertion of 90 nucleotides of extra sequence near or at the 5' end of their respective cDNAs. The analysis of this inserted sequence found that it was located at the position where intron-1 of the canine COX-1 gene would be predicted to be located based on the position of this intron in mouse and human COX-1 genes. Moreover, it was determined that the retained 90-nucleotide sequence in these canine cDNAs showed striking sequence similarity to intron-1 in human and mouse COX-1 genes and contained and 3' consensus splice sites indicative of a retained intron. The present study shows that these novel transcripts reflect an in-frame retention in the mRNA of intron-1 which would be predicted to cause significant changes in the biochemical properties of the COX-related protein encoded by these cDNAs.

[00241] Of the three intron-1 containing clone identified, one was found to contain, in addition to the 90-nucleotide insertion, an approximately 657 bp in-frame deletion. This inframe deletion corresponded approximately to the removal of exons 5-8 of the COX-1 message. Additionally, one codon appears to be deleted from the 5' end of exon 4 and another codon appears to be added from the 3' end of exon 8. This deletion is predicted to remove parts of the catalytic domain that might decrease peroxidase activity and might alter, but not destroy the fatty acid oxygenation activity of the enzyme encoded by this enzyme.

[00242] COX-1 variants COX-3, PCOX-la, hCOX-3(cc), hCOX-3(af), hCOX-3 (dell0) and hCOX-3(cs)) contain an in-frame insertion of intron-1. Insertion of this sequence in these RNAs occurs 2 amino acid residues downstream from the initiating methionine of the protein and results in the addition of about 30 amino acids into the signal peptide. This addition may change the subcellular location of this enzyme in the cell. In particular, it is predicted to target this protein to specific organelles, such as the endoplasmic reticulum, nuclear envelope, lipid bodies or of the membrane structures in the cytoplasm where the enzyme would bind to cytosolic surfaces of cell membranes by virtue of its retained membrane binding domain. The location of these enzymes to the cytosolic surface of cellular membranes or lipid bodies would be predicted to alter folding of the protein since it would lack glycosylation provided by microsomal enzyme. Also the enzyme would contain approximately 60 amino acids at to its amino terminus that would not normally be in this protein. This addition, itself, would alter folding and likely prevent dimerization. The present data indicate that a COX-1 variant protein, although containing all or significant 72 WO 03/029411 PCT/US02/30947 portions of the COX-1 sequence, would have different enzymatic properties then those of the COX-1 proteins.

[00243] One example of a COX-1 variant includes PCOX-1 a which exhibits a significant (219 amino acid) deletion in addition to having an insertion ofintron -1 at its amino terminus.

This enzyme possesses structural motifs for binding heme, having peroxidase activity, and oxygenating fatty acids similar to PIOXs. This means that, unlike COX-1 and COX-2, PCOX-la will not likely produce products such as prostaglandins that contain cyclopentane rings, since formation of such products require interaction of the fatty acid with hydrophobic residues deleted in PCOX-la. Instead, it is likely that PCOX-la forms monooxygenated hydroperoxy- or hydroxy- derivatives of fatty acids similar to PIOXs.

[00244] The structure of the COX-1 gene is known in human and mouse. Analysis of the structure ofintron-1 in these species show that both organisms contain an intron-1 that is similar in size to that in dogs which, when retained, would provide an in-frame insertion into the signal peptide encoding the protein (Figure Four amino acids (ArgGluXAspPro) at the amino terminus of this intron are conserved in all three species. RNA's were analyzed by Northern blot using oligonucleotide antisense probes specific to intron 1. Canine tissues were analyzed with a oligonucleotide (50 bp in length) found in intron 1. It detected specific RNA species containing this intron in a variety of tissues, including extensively in brain (Figure 8).

RNA isolated from a variety of human tissues were analyzed by Northern Blot using an antisense oligo (50 nucleotides in length) to intron-1. Washing conditions for this blot included two 30- minute washes at a temperature -20 degrees below the calculated melting temperature (Tm) of the probe. This was followed by one 10 minute wash at 4 0 C degrees below the calculated melting temperature. This high degree of stringency predicts an authentic rather than non-specific interaction of the probe with any interacting RNA. A 5.2 kb RNA was detected by the intron-1 specific oligonucleotide probe in human tissues of the forebrain, particularly the cortex, as well as in heart, muscle, liver, placenta, kidney and pancreas. The amygdala, hippocampus, whole brain, and lung and other tissues showed low expression of this RNA. In addition to the 5.2 kilobase transcript, several smaller RNAs of ~2-2.8 kb were detected by the probe in the cortex and other regions of the brain.

[00245] To further assure that intron-1 containing COX-1 transcripts exist in humans, reverse transcription coupled PCR was performed using RNA from human cells and tissues.

Amplification of a predicted ~1.8kb fragment was achieved using a forward primer located in intronl of the human gene and a reverse primer located immediately 3' to the predicted stop codon of the message. This amplicon hybridized in a Southern blot procedure with canine 73 WO 03/029411 PCT/US02/30947 COX-1 cDNA. In the Southern blot procedure the blot was washed at several times at 65 0

C

in 2X SSC.

[00246] Antisense oligonucleotides to the first intron of human and canine cyclooxygenase (COX)-1 genes were synthesized and end-labeled using (y- 32 P)-dATP. A canine cerebral cortex cDNA library was screened using a -1.0 kb canine COX-1 fragment by reverse transcription-coupled PCR (RT-PCR). The library was also screened with a P-labeled canine COX-1 intron 1 antisense oligonucleotide. Two full-length clones were isolated, completely sequenced, and designated COX-3 and PCOX-la. Both were derived from the canine COX-1 gene but retain intron 1. PCOX-la also has a 657 bp in-frame deletion spanning exons 5-8.

[00247] Canine cerebral cortex cDNA was synthesized, and primers were designed for PCR amplification. The sense primer (5'-CGGATCCGCCGCCCAGAGCTATGAG-3' (SEQ ID NO:7)) corresponded to nucleotides 15-32 of canine COX-3 sequence (submitted to GenBank under accession no. AF535138), with the 3' end of the primer being 2 nucleotides downstream of the initiating methionine. The antisense primer CGCCATCCTGGTGGGGGTCAGGCAC ACGGA-3' (SEQ ID NO:8)) corresponded to nucleotides 1865-1894, located 32 nucleotides upstream of the stop codon.

[00248] Northern blot analysis of human tissues with an intron-1 probe detected an ~5.2 kb mRNA. Marathon-readyTM human cerebral cortex cDNA (Clontech) was amplified by PCR (Clontech Advantage® 2 PCR enzyme system) using 5' and 3' primers, and a -4.2 kb amplified fragment was recovered and found to contain the entire coding region of human COX-1 with intron 1 retained.

[00249] Both COX-3 and PCOX-la were cloned into the baculovirus expression vector pBlueBac 4.5/V5-His (Invitrogen). Sf9 cells x 106) were infected with viral stocks at a multiplicity of infection (MOI) of 3 for expression of COX-3, PCOX-la, mouse COX-1 and mouse COX-2.

[00250 Total protein (20 gg) from human aorta was analyzed by Western blotting, using COX-1 monoclonal antibody (MAb) (Cayman Chemical, Ann Arbor, MI) and COX-3 antipeptide polyclonal antibodies (PAb). Primary antibodies were either preincubated with a mixture of human and mouse COX-1 intron 1 peptide (described below) for 1 hr, 4°C, or left unblocked. Blots were processed with appropriate rabbit-anti-mouse secondary antibody (1:2000) or goat-anti-rabbit secondary antibody (1:10,000) from Sigma. Densitometry of the autoradiographic image was performed using the AlphalmagerTM 2000 Documentation and Analysis System (Alpha Innotech Corporation).

74 WO 03/029411 PCT/US02/30947 [00251] Tunicamycin was added to a final concentration of 10 gg/ml to insect cells 1 hr after infection with baculovirus constructs. The cells were cultured and harvested after 48 hr.

COX activity of intact cells was determined by radioimmunoassay (RIA) (Salmon, 1978).

COX activity in intact Tu-treated cells was compared with activity in untreated cells infected with the appropriate virus (MOI 3).

[00252] Sf9 cells were infected with a high titer viral stock at a MOI of 3 and cultured for 48 hr. Infected cells expressing COX-3 were aliquoted into tubes x 106 cells) and centrifuged (1000 x g, 5min). The supernatant was discarded and the cell pellet resuspended in 100 ptl serum-free media containing the drug to be tested and preincubated at room temperature for 30 minutes. Arachidonic acid (100 pl, final concentration 5 or 30 pM) was then added, mixed and incubated (37°C, 10min). Samples were then centrifuged and 100 tl of the supernatant was assayed for COX activity by RIA for PGE 2 Assays were performed multiple times in triplicate. Inhibition curves were constructed and IC 50 values were determined using Prism® 3.0 (GraphPad, San Diego).

[00253] Peptides corresponding to the first 13 amino acids of human and mouse COX-3 primary sequence, as predicted by genomic clone sequences, were synthesized and coupled to keyhole limpet hemocyanin. A mixture of the human (MSRECDPGARWGC (SEQ ID and mouse (MSREFDPEAPRNC (SEQ ID NO:21)) peptides were injected into New Zealand white rabbits. The resulting polyclonal antibodies were then affinity purified using the above peptides immobilized on a Sulfolink T M coupling gel (Pierce) according to the manufacturer's instructions.

00254] Northern blot analysis detected a -5.2 kb mRNA containing intron 1 (Fig. panel The antisense primer (HCLE: ATAGGCCACCGGATGGAAGGA-3' (SEQ ID NO:9)) was designed from the 3' end of the published sequence and the sense primer (HCF: GCACCCCAGCA-3' (SEQ ID NO:17) from a site 5 nucleotides upstream from the initiation codon of the human COX-1 gene (Gen-Bank, accession number L 08404). The primers were designed with a BamHI recognition sequence at their 5' ends to facilitate cloning.

[00255] Marathon-ready TM human cerebral cortex cDNA (Clontech) was amplified by PCR (Clontech Advantage 2 PCR enzyme system) using the above primers. The resulting -4.2 kb amplified fragment was recovered from a low melting agarose gel and reamplified using nested primers (sense, HCEI: 5'-CGGATCCGCGCCATGAGCC GTGA-3' (SEQ ID NO: 18); antisense, HCS: 5'-CGGATCCTCAGAGCTCTGTGGATGGTCGCT-3' (SEQ ID WO 03/029411 PCT/US02/30947 NO:19). The resulting fragment kb) containing the entire coding region of human COX-1 (with intron 1 retained) was then cloned in the plasmid Bluescript and sequenced.

[00256] Two distinct mRNA species and ~1.9 kb) were detected on a Northern blot with a canine COX-1 coding region cDNA probe utilizing RNA isolated from canine cerebral cortex (Fig. 10, panel A, lane To further investigate these transcripts, a canine cerebral cortex cDNA library was constructed and the non-amplified library was screened as described above. Eleven clones were isolated and subsequently characterized by automated DNA sequencing. All of the eleven clones were found to contain canine COX-1 cDNA sequence. However, three clones harbored an insertion of 90 nucleotides at, or near, the end of their respective cDNAs, which showed 75% sequence identity to intron 1 of either human or mouse COX-1 genes. This extra sequence also contained 5' and 3' consensus splice sites indicative of a retained intron. In addition to the retention of intron 1, one of the three clones had a 657 bp in-frame deletion corresponding to exons 5-8 of the COX-1 message.

[00257] To determine whether the two previously detected COX mRNA transcripts (i.e.

-2.6 and -1.9 kb) harbored intron 1, the Northern blot experiment was repeated utilizing a radiolabeled antisense canine COX-1 intron 1-specific oligonucleotide probe (CCI) (Fig. panel A, lane Importantly, the -1.9 kb mRNA transcript and the -2.6 kb transcript were detected suggesting that novel COX-1 mRNA splice variants were indeed expressed in canine cerebral cortex. Therefore the novel COX cDNA clone, which harbored a non-spliced intron 1 and corresponded to the -2.6 kb mRNA transcript has been designated as COX-3.

Additionally, the novel COX cDNA clone which harbored intron 1, lacked exons 5-8, and corresponded to the -1.9 kb mRNA transcript, has been designated partial COX-la or PCOXla (Fig. 11).

[00258] Reverse transcription-coupled PCR of canine cerebral cortex RNA as well as analysis of Northern blots, indicated that COX-3 mRNA is present in this brain region at about 5% of the level of COX-1 mRNA (Fig. 10, panel Interestingly, these analyses also demonstrated that the ~1.9 kb mRNA corresponding to PCOX-la was actually a mixture of two mRNAs that differed in size by -90 nucleotides (Fig. 10, panel One of these mRNAs was PCOX-la and the other (PCOX-lb) was identical to PCOX-la except that PCOX-lb lacked intron 1. PCOX-la and PCOX-lb are expressed in equal amounts in brain cortex (Fig.

panel B).

[00259] To determine whether novel COX-1 related mRNA transcripts were also expressed in human tissues, human Northern blot experiments were performed utilizing a human-intron-1 specific (HCI) probe. Importantly, these results demonstrated the existence of 76 WO 03/029411 PCT/US02/30947 a novel -5.2 and -2.8 kb mRNA transcripts (Fig. 10, panel Faint hybridization signals were also seen around 1.9 kb. Hybridization of HCI to the ~5.2 kb form was tissue-specific, with highest levels present in the cerebral cortex followed by the heart. These observations differ from the characterized expression patterns of COX-1 mRNA.

[00260] COX enzymes are intralumenal residents of the endoplasmic reticulum and depend on N-linked glycosylation for proper folding and activity. Retention ofintron 1 could prevent COX-3 and PCOX-1 expression by preventing export of these mRNAs from the nucleus or by targeting these proteins to another subcellular compartment, preventing glycosylation. Therefore, insect cells (Sf9) were infected with recombinant baculovirus expressing COX-3, PCOX-1, and COX-1 and cell homogenates were assayed for protein expression by Western blotting. Antibodies specific for the conserved amino acid sequence (MSREXDPXA) predicted to be encoded by intron 1 in mammals were used to probe for COX-3 and PCOX-la and b. This analysis demonstrated that both COX-3 and PCOX-1 are efficiently expressed in insect cells. No detectable products resulting from removal ofintron 1 by splicing were detected immunologically or by RT-PCR analysis of RNA extracted from infected Sf9 cells. Moreover, the signal peptide, which in COX-3 and PCOX-la or b contains an additional intron 1 encoded sequence, was not removed by signal peptidase as it is in COX-1 and COX-2.

[00261] Posttranslational N-linked glycosylation of COX-3 and PCOX-1 was compared to that of COX-1 using tunicamycin to inhibit core glycosylation. Immunoblot analysis demonstrated a decrease in or disappearance of glycosylated forms of COX-3, PCOX-1, and COX-1 (Fig. 12 Top; left, middle and right panels, respectively). Expression systems were then assayed for cyclooxygenase activity by measuring the production of PGE 2 in whole insect cells. COX-3 activity was found to be -20% of that of COX-1 and PCOX-1 completely lacked detectable COX activity (Fig. 12 bottom panels). COX activity in cells treated with tunicamycin was found to be significantly decreased or abolished by this drug, indicating that N-linked glycosylation is necessary for COX activity of COX-3.

00262] RNA studies in human tissues indicated highest levels of COX-3 message to be in the cerebral cortex and heart. Western blot analysis of human aorta (Fig. 15) using either COX-1 monoclonal antibody or COX-3 antipeptide polyclonal antibody detected the presence of distinct 65 and 53 kDa COX-1 related proteins. Additionally, the COX-1 but not COX-3 antibody, detected a 69 kDa protein, corresponding to glycosylated COX-1, as well as a 50 kDa protein, which may represent a proteolytic fragment of COX-1 or PCOX-lb.

Detection of both of the 65 and 53 kDa proteins was selectively reduced by preincubation of 77 WO 03/029411 PCT/US02/30947 the anti-peptide sera with its cognate peptide, whereas detection of the same proteins by the COX-1 monoclonal antibody was unaffected by this treatment.

00263 Analgesic/antipyretic drugs and NSAIDs were tested for their ability to inhibit COX activity of COX-3 as compared to their ability to inhibit COX-1 and COX-2. Analyses were done in the presence of exogenously added arachidonic acid at 30 and 5 pM concentrations. At the higher concentration of substrate, only COX-3 was inhibited by acetaminophen (Fig. 13, panel Moreover, COX-3 was found to be significantly more sensitive to acetaminophen than either COX-1 or COX-2 at the lower substrate concentration (Fig. 13, panel Acetaminophen inhibited COX-3 at an IC 5 0 value of 64 gM when done in the presence of 5 atM arachidonic acid, whereas IC 5 o values for COX-1 and COX-2 were 2.1and 92.4-fold higher, respectively.

[002641 Acetaminophen is considered to be the active metabolite of phenacetin, a once popular analgesic/antipyretic drug that is no longer extensively used due to the occurrence of methemoglobinemia, renal toxicity, and suspected renal and bladder carcinogenesis.

Phenacetin is rapidly O-de-ethylated in the body to form acetaminophen and is further metabolized to other minor but toxic compounds. Thus only small levels of of phenacetin circulate in the blood. Interestingly, however, phenacetin was much more potent at inhibiting COX-3 than was acetaminophen (Fig. 13, panel Under substrate conditions of 30 pM, phenacetin inhibited COX-3 at an IC5o value of 102 M as opposed to 460 pM for acetaminophen tested under similar conditions. As with acetaminophen, phenacetin preferentially inhibited COX-3.

00265] Another analgesic/antipyretic drug, dipyrone, was also significantly more potent at inhibiting COX-3 than either COX-1 or COX-2 (Fig. 13, panel Dipyrone inhibited COX-3 with an IC 50 value of 52 iM and COX-1 at a 6.6-fold higher concentration. No detectable inhibition of COX-2 by dipyrone was observed below 1 mM. Dipyrone is a prodrug that spontaneously breaks down in aqueous solutions to a variety of structurally related pyrazolone compounds that differ in their potency as analgesic/antipyretic agents. Antipyrine and dimethylaminopyrene are similar to two breakdown products of dipyrone, and possess markedly reduced therapeutic potency and similarly show markedly reduced inhibition of COX-3 as compared to dipyrone (Table However, these compounds, like other analgesic/antipyretic agents, preferentially inhibit COX-3.

[0 02 6 6] COX-3 was also found to differ in its sensitivity to inhibition by a selection of NSAIDs. Diclofenac was the most potent inhibitor of COX-3 tested and diclofenac, aspirin WO 03/029411 PCT/US02/30947 and ibuprofen preferentially inhibited COX-3 over COX-1 and COX-2. The ICso values of these drugs are tabulated (Table Importantly, the overall results indicate that COX-3 possesses a COX activity which differs pharmacologically from both COX-1 and COX-2.

[00267] Both COX-3 and PCOX-la are formed by intron retention. We have previously shown that COX-2 in chicken is regulated by intron 1 retention, similar to that seen with COX-3. Unspliced mRNAs are largely retained in the nucleus. In the case of chicken COX- 2, retention of intron 1 prevents translation and nuclear export of the mRNA. However, both COX-3 and PCOX-la mRNAs in insect cells retain the intron and are exported from the nucleus and are translated (Fig. 12). The polypeptides produced from COX-3 and PCOX-la include sequence encoded by the intron 1 and are functionally different from fully-spliced COX-1. Therefore retention of intron 1 provides a mechanism by which a novel COX enzyme, COX-3, can be produced in cells and tissues. Consistent with the concept that retention of intron 1 is important in creating COX-3 and/or regulating COX-1 is the finding that the DNA sequence of intron 1 from dog, human, and mouse COX-1 genes displays a high degree of conservation. This is most evident in the 5' and central regions of the intron.

Overall intron 1 shows 41% sequence identity between all three species with the sequence GCCTcNGGNGGAGCCTYGAAYGCYAG-3' (SEQ ID NO:44) in the central region of the intron being highly conserved. In fact intron 1, is more conserved in these species than is exon 1, suggesting that intron 1 plays an important and similar role in mammals. Highly conserved elements of intron 1 may also play a role in regulation of its retention. Further buttressing the concept that intron 1 plays an important role in regulating COX-3 expression is the fact that the gene structure of COX-1 and COX-2 differ only in their placement of intron 1. COX-1 has 10 introns while COX-2 has 9. The additional intron in the COX-1 gene is intron 1, which is retained in COX-3.

[002 68 COX-3 shares all the catalytic features and important structural features of COX-1 and COX-2. However, the insertion of intron 1, two amino acids downstream from the initiating methionine would result in the addition of 30 amino acids to the signal peptide.

Despite having a signal peptide and intron-l-encoded sequence retained, COX-3 co-migrates with COX-1 in SDS-PAGE gels. It also appears to enter the endoplasmic reticulum where it is glycosylated and its glycosylation is required for activity. In insect cells COX-3 shows approximately 20% of the activity of COX-1, which in turn exhibits about 20% of the activity of COX-2. COX-1, COX-2, COX-3, and PCOX-la all show equivalent expression in our baculovirus system, and so a lowered ability of insect cells to express active COX-1 relative to COX-2 may be due to the inability of insect cells to posttranslationally process COX-1 79 WO 03/029411 PCT/US02/30947 correctly. Subcellular localization studies done by differential centrifugation demonstrate that neither COX-3 nor PCOX-la is cytosolic. Membrane binding of both proteins is predicted from the fact that both retain a membrane binding domain and both appear to enter the lumen of the endoplasmic reticulum. Retention ofintron 1 could alter folding and may affect dimerization and the active site. These effects could be through structural changes or altered protein targeting. COX-1 site-directed mutagenesis of either Cys 313 or Cys 5 40 both of which are more than 25 A from the heme iron, was observed to reduce the activity of the enzyme by 80-90%. Therefore, although COX-3 contains all of the COX-1 sequence, the retained intron sequence could significantly alter its enzymatic properties. The present inhibition studies of COX-3 indicate this to be the case.

[00269] The present studies shows that the COX-1 variant COX-3 is sensitive to drugs that are analgesic/antipyretic, but which have low anti-inflammatory activity. Pain and fever have many etiologies that employ complex cellular and biochemical pathways. The finding that COX-3 is sensitive to analgesic/antipyretic drugs suggests that the COX-1 gene plays an integral role in pain and/or fever. Depending on the physiological context, pain pathways involve products from either the COX-1 or COX-2 genes. COX-2 selective drugs, for example, are clinically useful in inhibiting inflammatory pain in humans and are more potent than COX-1-selective NSAIDs at inhibiting pain induced by pro-inflammatory agents (e.g.

carrageenan) in some paw inflammation assays in rodents. COX-1 selective drugs, in contrast, are superior to COX-2-selectivc agents at inhibiting visceronociception caused by a variety of chemical pain stimulators. Moreover, Ballou et al. (Proc. Natl. Acad. Sci. USA 97:10272, 2000) found that visceronociception was greatly decreased in COX-1 but not COX-2 knockout mice. Both COX-1 and COX-2, on the other hand, have been implicated in nociception models that measure analgesia outside the gut, such as in formalin and urate crystal tests. A role for COX-1 in pain is further supported by the fact that COX-1-selective NSAIDs aspirin, ketorolac, ketoprofen, ibuprofen, and suprofen are clinically important analgesic agents in humans and animals). Despite their relative exclusion from the brain, these drugs may reach sufficient concentration to effect COX-3 in the brain.

Furthermore, the analgesic effects of these drugs often occur at significantly lower doses than those needed to inhibit inflammation. Clinical and experimental association of COX-1 and pain may be functionally explained by the finding that COX-1 is a marker for subpopulations of putative nociceptor neurons in the dorsal root ganglion.

[00270] With regard to pyresis, COX-2 but not COX-1 knockout mice demonstrate reduction in LPS- and interleukin-l-induced fevers, and some new COX-1 selective WO 03/029411 PCT/US02/30947 inhibitors, such as SC-560, have proven ineffective at inhibiting LPS-induced fever in animal models. Clinically, rofecoxib, a COX-2 selective inhibitor, inhibits naturally occurring fever and also inhibits the maintenance of fever in animal models. Yet aspirin, a COX-1 preferential inhibitor is one of the most effective antipyretic NSAIDs, and inhibits fever at doses ranging from 5-15 mg/kg, far below the 60-80 mg/kg used to treat inflammatory disease. Furthermore, nimesulide, a COX-2 preferential inhibitor, was found to be antipyretic in dogs only at plasma concentrations that would also inhibit COX-1. Thus a role for COX-1 in fever may exist.

[00271] The mechanism of action of acetaminophen has been unknown and postulated to be through inhibition of a brain COX that has never been identified. Northern blot analysis and cDNA cloning show that COX-3 is expressed in canine brain. COX-3 also appears from Northern blot studies (Fig. 10) to be expressed in specific regions of the human brain, in particular cerebral cortex. Moreover, our studies using ectopically expressed COX-3 in insect cells demonstrate that COX-3 is significantly more sensitive to acetaminophen than COX-1 and COX-2. Under physiological conditions, where steady-state acetaminophen concentrations reach approximately 100 tM, and where free arachidonic acid levels are 1only COX-3 is predicted to be appreciably inhibited. These findings suggest that inhibition of COX-3 in brain and the spinal cord could be the long sought-after target for acetaminophen.

[00272] The proposed mechanism of action for acetaminophen inhibition of COX-3 also appears to extend to pyrazolone drugs such as dipyrone and related compounds aminopyrine and antipyrine. Dipyrone is a potent analgesic/antipyretic drug which, like acetaminophen, lacks antiinflammatory activity. Dypyrone however is structurally unrelated to acetaminophen. Consistent with COX-3 being the target for analgesic and antipyretic drugs is the finding that these structurally dissimilar agents preferentially inhibit COX-3 and that their therapeutic potencies follow their ability to inhibit COX-3. The ICso values are as follows: dipyrone (52 pM), 4-dimethylaminoantipyrine (688 uiM), and antipyrine (862 pM). Only dipyrone is therapeutically effective as an analgesic/antipyretic drug. Its active breakdown product, 4-methylaminoantipyrine reaches concentrations of 104 gM and 86 RM in plasma and the central nervous system, respectively. Thus, COX-3 inhibition occurs at known physiological concentrations ofpyralazone drugs as well as acetaminophen. Additionally, inhibition of COX-3 does not require addition of glutathione, epinephrine, or other exogenously added "cofactors" which have been required in other systems.

WO 03/029411 PCT/US02/30947 [00273] Analgesic/antipyretic drugs inhibit COX-3 activity at higher concentrations than standard NSAIDs. From a therapeutic standpoint this may be rationalized by the fact that these drugs penetrate the blood brain barrier well, thus accumulating in the CNS at high enough concentrations to inhibit COX-3. Analgesic/antipyretic drugs, like acetaminophen, have long been postulated to have a central mechanism of action. Carboxylate-containing NSAIDs, on the other hand, cross the blood-brain barrier poorly and have a well-defined ability to reduce pain peripherally by reducing prostaglandin synthesis that sensitizes nociceptors. Several central analgesic mechanisms of action for NSAIDs have also been proposed wherein inhibition of prostaglandin synthesis in brain or spinal cord, potentially via COX-3, could contribute to the analgesic action of NSAIDs. Thus, action of NSAIDs in the body is likely to be central (COX-3) as well as peripheral (COX-1, COX-2 and COX-3).

COX-1 variants in the CNS may be an essential target of both analgesic/antipyretics and standard NSAIDs.

[00274] A comparison of COX-3 inhibition by analgesic/antipyretics and NSAIDs in these studies (Fig. 13 and Table 1) suggest that both types of drugs may be capable of modulating a COX-variant activity COX-3). Table 1 shows IC50 values of selected analgesic/antipyretic drugs and NSAIDs. Also shown are relevant inhibition ratios of COX- 1/COX-3 and COX-2/COX-3 indicating preferential inhibition towards COX-3. All assays were carried out at 30 mM arachidonic acid. Asterisks in the table indicate the following notations: 4-dimethylaminoantipyrine; no detectable inhibition at ImM; ratios not applicable.

WO 03/029411 PCT/US02/30947 Table 1 DRUG ICso, PM COX-1 COX-2 COX-3 Acetaminophen >1000 >1000 460 Aminopyrine* >1000 >1000 688 Antipyrine >1000 >1000 863 Aspirin 10 >1000 3.1 Diclofenac 0.035 0.041 0.008 Dipyrone 350 >1000 52 Ibuprofen 2.4 5.7 0.24 Indomethacin 0.010 0.66 0.016 Phenacetin >1000 >1000 102 Caffeine >1000 >1000 >1000 Thalidomide >1000 >1000 >1000 [00275 Comparison of COX-1, COX-2 and COX-3 demonstrated that COX-3 is most like COX-1 in its sensitivity to NSAIDs but is significantly more sensitive to many drugs, such as diclofenac and ibuprofen, and less sensitive to others like sodium salicylate than is either COX-1 or COX-2. The higher sensitivity of COX-3 to NSAID inhibition may allow it to be preferentially inhibited in the CNS by low levels of NSAIDs that cross the blood-brain barrier. Furthermore, the differential sensitivity of COX-3 to analgesic/antipyretic drugs and NSAIDs suggests that highly selective inhibitors can be made for COX-3.

[00276] Human COX-3 is mainly expressed as a -5.2 kb mRNA and has a tissue-specific pattern of expression (Fig. 10, panel This -5.2 kb mRNA is an alternatively polyadenylated human COX-1 message previously reported and partly characterized in its 3' region It appears, therefore, that the retention ofintron 1 may influence the site at which the mRNA is polyadenylated. This finding suggests that the 3' untranslated regions of the mRNA may play a functional role in expression of COX-3 and perhaps PCOX-la. The functional significance and the mechanism by which intron retention and alternative polyadenylation are coordinated need to be elucidated. It is also interesting to note that the -5.2 kb mRNA has been shown to be regulatable (36) and hence may be regulated in response to physiological stimuli and signal transduction. Indeed, the levels of COX-3 mRNA in human and canine cerebral cortex are relatively low. This may be due to cell type- WO 03/029411 PCT/US02/30947 specific expression such as has been shown for COX-1 immunoreactive protein in a subpopulation of putative nociceptor neurons However, COX-3 in human will require further experimentation since some of the published sequences differ by one nucleotide in intron 1 and hence are out of frame. These may constitute genuine polymorphisms or sequencing errors. Alternatively, intron 1 may be out of frame in humans, requiring other mechanisms such as ribosomal frame shifting to produce a functional COX-3 protein.

[00277] The present studies have identified novel COX-1 variants, including COX-3 protein of about 65 kDa in human aorta and a PCOX-la protein of about 53 kDa. These proteins are detected by both COX-3 antipeptide polyclonal antibody and a COX-1 monoclonal antibody and appear to be present at about 25% of the level of COX-1. The kDa protein is smaller than would be predicted if the protein is glycosylated to the same extent as COX-1, suggesting hypoglycosylation or other differences exist between the 65 kDa protein and COX-1. The 53 kDa proteins are present as a doublet, and are of a higher molecular weight than that predicted by the PCOX-1 a protein primary sequence. This suggests that, like canine PCOX-1 a expressed in insect cells, the human protein may be glycosylated, and that different glycosylation states may exist giving rise to the doublet observed. A 50 kDa protein is also detected only by the COX-1 monoclonal antibody, and is a candidate for being PCOX-lb. It appears to be present at about 15% of the level of COX-1.

[00278] PCOX-la is identical to COX-3 except for a deletion of 219 amino acids in the catalytic domain of the protein, corresponding to exons 5-8. It lacks detectable cyclooxygenase activity, as shown by its inability to make prostaglandins from arachidonic acid. The deleted portion contains structural helices HE, H1, H2, H3, H5, and part of H6 defined for COX-1 and COX-2. Of these helices, H2 and H5 form part of the core peroxidase catalytic site. Because of the lack of H2 and H5, PCOX-1 most likely lacks detectable peroxidase activity. In this way it is similar to plant PIOX enzymes and Gaeumannomyces graminis linoleate diol synthase (LDS), which also lack peroxidase activity. They do, however, have fatty acid oxygenase activity that is similar in mechanism to the oxygenase activity of cyclooxygenase, and contain sequences similar to those found in COX-1 and Figure 14 shows an alignment of H2, H5, and H8 (helix containing Tyr 38 and the proximal histidine) from the consensus sequences of COX-1 and -2 with PIOXs and

LDS.

[00279] Although the peroxidase activity of cyclooxygenase is needed to create the protein radical used in the cyclooxygenase reaction, continued peroxidase activity is not essential for continued cyclooxygenase activity. After the enzyme has been primed by one 84 WO 03/029411 PCT/US02/30947 peroxidase reaction, it can continue to catalyze oxygenation of the substrate, because the tyrosine radical is regenerated after each oxygenation reaction. This priming mechanism for cyclooxygenase also seems to work with PIOXs and LDS. The active site tyrosine and proximal histidine of cyclooxygenase are conserved in PIOXs and LDS. It is believed that these enzymes have a reaction mechanism similar to COX, based on their similarity with cyclooxygenases. It is likely, then, that they do retain a low level of peroxidase activity that, although undetectable, is sufficient to prime them for oxygenase activity.

[00280] Because only one turnover of the peroxidase active site is required for cyclooxygenase activity in COX-1 and there may be enough residual peroxidase activity in PCOX-1 proteins to prime them. However, we have shown that PCOX-la does not have cyclooxygenase activity. It is possible, based on comparison with PIOXs that PCOX-1 proteins do retain lipid oxygenase activity, similar to the lipid oxygenase activity of PIOXs.

Further studies are required to determine what the substrate of PCOX-1 proteins would be.

[00281] Because PCOX-la and PCOX-lb are missing such a large portion of its catalytic domain, it is possible that it needs to be bound to another protein for it to be catalytically active. We have previously found that cyclooxygenases bind to nucleobindin (Ballif, 1996).

Nucleobindin is a candidate for binding to PCOX-1 proteins as well. Additionally, a form of COX-1 has been described that co-localizes with prostacyclin synthase in filamentous structures of cultured ehdothelial cells. This filamentous form of COX-1 has no cyclooxygenase activity, and is a candidate for being a PCOX-1 protein.

[00282] Human COX-3 is mainly expressed as a -5.2 kb mRNA and has a tissue-specific pattern of expression (Fig. 10, panel This -5.2 kb mRNA is an alternatively polyadenylated human COX-1 message and partly characterized its 3' region. The data provided herein indicates that retention ofintron 1 influences the site at which the mRNA is polyadenylated. The functional significance and the mechanism by which intron retention and alternative polyadenylation are coordinated need to be elucidated. It is also interesting to note that the -5.2 kb mRNA has been shown to be inducible and may be regulated in response to physiological stimuli and signal transduction. Indeed, the levels of COX-3 mRNA in human and canine cerebral cortex are relatively low and may be due to cell typespecific expression requiring specific signals. However, COX-3 in human will require further experimentation since some of the published sequences differ by one nucleotide in intron 1 and hence are out of frame. These may constitute genuine polymorphisms or sequencing errors. Alternatively, intron 1 may be out of frame in humans, requiring other mechanisms such as ribosomal frame shifting to produce a functional COX-3 protein. The WO 03/029411 PCT/US02/30947 finding that retention ofintron I is coordinately tied to alternative polyadenylation suggests that the 3' untranslated regions of the mRNA may play a functional role in expression.

[00283] A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention.

Claims

1. An isolated nucleic acid molecule comprising intron 1, or fragment thereof, of cyclooxygenase type 1, wherein the nucleic acid molecule is RNA.

2. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule is mRNA.

3. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule is cDNA.

4. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule encodes a polypeptide comprising at least one domain that catalyzes the cyclization and/or oxygenation of a fatty acid radical, at least one membrane-binding domain, and at least one heme binding domain.

5. The nucleic acid of claim 1, wherein the nucleic acid molecule encodes a polypeptide selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16.

6. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule comprises SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: SEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 13.

7. An isolated nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 1; b) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 3; c) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 4; d) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 6; e) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: f) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 11; g) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 12; and h) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO: 13.

8. An isolated nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 2; b) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: c) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 14; (R:\LIBF]45527a.doc:LNB

24-APR2007 16:37 SPRUSON FERGUSON 92615486 NO. 7698 P. 13/19 88 a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 15; and e) a nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 16. S9. An isolated nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule which encodes a polypeptide comprising the Samino acid sequence of SEQ ID NO: 2, wherein the nucleic acid molecule hybridizes to a SQ IDNO: 4 o der stringent conditio and o nucleic acid molecule comprising SEQ ID NO: 1 or 3 under stringent conditions;and Sb) a nucleic acid molecule which encodes a polypeptide comprising the to a, ino acid sequence of SEQ ID NO: 5, wherein the nucleic acid molecule hybridizes to a o nucleic acid molecule comprising SEQ ID NO: 4 or 6 under stringent conditios. An isolated nucleic acid molecule which hybridizes to the nucleic acid molecule of any one of claims 7, 8, or 9 under stringent conditions. 11. An isolated nucleic acid molecule comprising a nucleotide sequence which is Is complemenuarY to the nucleotide sequence of the nucleic acid molecule of any one of claims 7 8, or 9. 12. An isolated nucleic acid molecule comprising the nucleic acid molecule of anyone of claims 7, 8, or 9 and a nucleotide sequence encoding a heterologous polypeptide. 2 o 13. A vector comprising the nucleic acid molecule of any one of claims 1, 7, 8, or 9. 14. The vector of claim 13, which is an expression vector, A host cell transfected with the vector of claim 13. 16. A method of producing a polypeptide comprising culturing a host cell transfected with the vector of claim 13 in an appropriate culture medium to, thereby, produce the polypeptide. D NO 17. An isolated polypeptide comprising the amio acid sequence of SEQ ID NO 2, 5, 14, 15 or 1 6 18. The polypeptide of claim 17, further comprising heterologous amino acid sequences. 19. An isolated antibody which selectively binds to a polypeptide of claim 17. A method for detecting the presence of a polypeptide of claim 17 in a sample comps:a) contacting the sample with a compound which selectively binds to the polypeptide; and 766360 .JIN COMS ID No: SBMI-07118661 Received by IP Australia: Time 16:39 Date 2007-04-24 24-APR.2007 16:37 SPRUSON FERGUSON 92615486 NO- 7698 P. 14/19 89 o b) determining whether the compound binds to the polypeptide in the sample to thereby detect the presence of a polypeptide of claim 17 in the sample 21, The method of claim 20, wherein the compound which binds polypeptide is an antibody.liv bin o o i of 22. A kit comprising a compound which selectivelbinds to a polypedeof claim 17 and instrIctions for use. 23. A method for detecting the presence of a nucleic acid molecule of any one of claims 1, 7, 8, or 9 in a sample comprising: rn a) contacting the sample with a nucleic acid probe or primer which c0 selectively hybridizes to the nucleic acid molecule; and 0 b) determining whether the nucleic acid probe or primer binds to a nucleic acid molecule in the sample to thereby detect the presence of a nucleic aid molecule of any one of claims 1, 7, 8, or 9 in the sample.e c ie d 24. The method of claim 23, wherein the sample comprises nRNA molecules and is is contacted with a nucleic acid probe. A kit comprising a compound which selectively hybridizes to a nucleic acid molecule of any one of claims 1, 7, 8, or 9, and instructions for use.

26. A method for identifying a compound which binds to a polypeptide of claim 17 comprising: a) contacting the polypeptide, or a cell expressing the polypeptide with a test compound; and b) detenining whether the polypeptide binds to the test compound.

27. The method of claim 26, wherein the binding of the test compound to the polypeptide is detected by a method selected from the group consisting of: a) detection of binding by direct detection of test compound/polypeptide binding; b) detection of binding using a competition binding assay; and c) detection of binding using an assay for activity.

28. A method for modulating the activity of a polypeptide of claim 17 comprising contacting the polypeptide or a cell expressing the polypeptide with a compound which binds to the polypeptide in a sufficient concentration to modulate the activity of the polypeptide.

29. A method for identifying a compound which modulates the activity of a polypeptide of claim 17 comprising: a) contacting a polypeptide of claim 17 with a test compound; and 766360_1.IN COMS ID No: SBMI-07118661 Received by IP Australia: Time 16:39 Date 2007-04-24 24, APR. 2007 16:38 SPRUSON FERGUSON 92615486 NO. 7698 P. 15/19 b) determiniLg the effect of the test compound on the activity of the polypeptide to thereby identify a compound which modulates the activity of the poypeptide.A method for preventing or treating Alzheimer's Disease in a subject, said method comprising administering to said subject an effective amount of a specific inhibitor of COX-1 variant activity, i a pharmaceutically acceptable carrier. S31. The method as in claim 30 in which said specific inhlibitor of COX-I variant oactivity is a specific inhibitor of COX-1 variant activity encoded by a nucleic acid as set eforth in claims 1, 7, 8, or 9. )0

32. A method for ameliorating a neurodegenerative condition in a subject, said a omethod comprising administering to said subject a specific inhibitor of cyclooxygenase type 1 activity encoded by a nucleic acid as set forth in claims 1, 7, 8, or 9, in a phartnaceutically acceptable carrier.

33. The method as in claim 32 wherein said neurodegenerative condition is stroke, cerebral ischemia, a demyelinating condition, or mechanical injury.

34. A method for treating imiuno or inflammatory conditions associated with Alzheimer's Disease in a subject, said method comprising administering to said subject a specific inhibitor of a COX-1 variant activity, in apharmaceutically acceptable carner. The method as in claim 34 in which said specific inhibitor of cyclooxygenase activity is a specific inhibitor of cyclooxygenase type 1 activity encoded by a nucleic acid as set forth in claims 1, 7, 8, or 9.

36. A method of modulating expression, production, or formation of amyloid precursor protein (APP) in a subject, comprising administering to said subject an effective amount of an antagonist, wherein said antagonist is a non-steroidal anti-inflammatory agent that is a specific inhibitor of a COX-I variant, in a pharmaceutically acceptable carier

37. The method as in claim 36 in which said specific inhibitor of cyclooxygenase activity is a specific inhibitor of cyclooxygenase type I activity encoded by a nucleic acid as set forth in claims 1, 7, 8, or 9.

38. A method of selectively inhibiting COX-3 or PCOX-la activity in a subject, comprising administering a compound that selectively inhibits activity of the COX-3 or PCOX-la gene product to a subject in need of such treatment.

39. The method of claim 38 in which the compound is a non-steroid anti- inflammatory compound. 766360,_1,AIN COMS ID No: SBMI-07118661 Received by IP Australia: Time 16:39 Date 2007-04-24 24. APR. 2007 16:38 SPRUSON FERGUSON 92615486 NO. 7698 P. 16/19 91 A method for selectively inhibiting COX-3 or PCOX-la activity in a subject, comprising administering a non-steroidal compound that selectively inhibits activity of the COX-3 or PCOX-l a gene product in a subject in need of such treatment, wherein the activity of the non-steroidal compound does not result in significant toxic side effects in Sthe subject. 41, A method for selectively inhibiting COX-3 or PCOX-la activity in a subject, comprising administering a non-steroidal compound that selectively inhibits activity of othe COX-3 or PCOX-la gene product in a subject in need of such treatment, wherein the ability of the non-steroidal compound to selectively inhibit the activity of the COX-3 or PCOX-Ia gene product is determined by: a) contacting a genetically engineered cell that expresses COX-3 or PCOX-la, and not COX-1 or COX-2, with the compound and exposing the cell to a pre- determined amount of arachidonic acid; b) contacting a genetically engineered cell that expresses COX-1 or COX- 1i 2, and not COX-3 or PCOX-la, with the compound and exposing the cell to a pre- determined amount of arachidonic acid; c) measuring the conversion of arachidonic acid to its prostaglandin metabolite; and d) comparing the amount of the converted arachidonic acid converted by 0 each cell exposed to the compound to the amount of the arachidonic acid converted by control cells that were not exposed to the compound, so that the compounds that inhibit COX-3 orPCOX-la and not COX-1 or COX-2 activity are identified.

42. A method of identifying a compound that modulates the activity of COX-1 variant, the method comprising: a) providing a cell transfected with a DNA encoding a COX-1 variant, wherein the DNA comprises intron 1 of a cyclooxygenase type 1, and wherein the cell expresses COX-1 variant; b) contacting said cell, in an intact or disrupted state, with a test compound; and c) determining whether the activity of COX-1 variant is decreased or increased in the presence of the test compound, wherein a decrease or increase in said COX-1 variant activity is an indication that the test compound modulates the activity of a COX-I variant, 766360_1JIN COMS ID No: SBMI-07118661 Received by IP Australia: Time 16:39 Date 2007-04-24 24-APR,2007 16:38 SPRUSON FERGUSON 92615486 NO- 7698 P. 17/19 92 S43. The method of claim 42, wherein the DNA encoding a COX-1 variant encodes an amino acid sequence as set forth in SEQ ID NO: 2, SEQ I NO: 5, SEQ ID NO: 14, SEQ ID NO 15 or SEQ ID NO: 16. ce 44. The method of claim 42, wherein the DNA encoding a COX-1 variant is selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 and SEQ ID NO: 13. The method ofclai42,herein the cell is a mammalian cell, or an insect O cell, or a bacterial cell..

46. The method of claim 42, herein the test compound is a non-steroid inflammatory drug.

47. A method for making a compound that modulates the activity of a COX- S t e co o ry comprii a btt aing a puity of adfse w at variant wherein the DNA encoding a COX-1 variant comprises intron 1 of a cyclooxygenase type 1, the method comprising in e ariout the method of claim 42 to identify a compound that modulates the activity of COX-1 variant and b) manfacid cted the compound.ofSEQIDNO SEQIDNo EQ NO:4,SEQ NO: An array comprising a substrate having a plurality of addresses, wherein at least one address of said plurality of addresses comprises a capture probe that can specifically bind a COX-1 variant nucleic acid o a fragment of said COX-1 varant nucleic acid wherein the DNA encoding a COX-1 variant comprises intron I of a o20 cyclooxygenae type 1.

49. The array of claim 48, wherein the COX-1 variant nucleic acid encodes an amino acid sequence as set forth in SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16. The array of claim 48, wherein the COX-1 variant nucleic acid is selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 1, SEQ ID NO: 12 and SEQ IDNO: 13.

51. An array comprising a substrate having a plurality of addresses, wheein at least one address of said plurality of addresses comprise a capture probe that can specifically bind intron 1 of a COX-1 variant nucleic acid.

52. The array of claim 51, wherein the COX-1 variant nucleic acid encodes an amino acid sequence as set forth in SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 14, SEQ ID NO: 15 or SEQ ID NO: 16.

53. The array of claim 51, wherein the COX-I variant nucleic acid is selected from the group consisting of SEQ IDNO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12 and SEQ IDNO: 13. 766360_1,IN COMS ID No: SBMI-07118661 Received by IP Australia: Time 16:39 Date 2007-04-24 24-APR.2007 16:39 24. PR. Q57 6:39SPRUSON FERGUSON 92615436NO763 P 1/9 NO. 7698 P. 18/119 93 o

54. A method of choosing a therapy for a subject, the me tho comprising: a) providing a plurality of reference expression profiles, each associated wit a therapy; 1-b) providing a nucleic acid obtained from a subject; sc) contacting the nucleic acid with an array of claim 53 or claim 56; d) detecting binding of the nucleic, to each address of the plurality of addresses to thereby provide a subject expression profile; and oe) selecting the reference profile most similar to the subject expression profile, to thereby choose a therapy for the subject. N 10 55. A kit for evaluating a pharmaceutical composition, the kit comprising: oa) ansarray of claimn48 orclaimf5 3 and b) a computer-readable medium having a plurality of expression profiles, wherein each profile of the plurality has a plurality of values, each value representing the expression of a COX-1 variant nucleic, acid detected by the array. is

56. A method of selecting a therapy for a subject, the method comprising: a) obtaining a subject sample from a caregiver; b) obtaining a nucleic acid from the subject sample; c) identifying a subject expression profile from the nucleic. acid; d) selecting from a plurality of reference profiles a matching reference 2o profile most similar to the subject expression profile, wherein the reference profiles and the subject expression profile have a plurality of values, each value representing the expression level of a CQX-l variant; e) wherein each reference profile of the plurality of reference profiles is associated with a therapy; and f) transmitting a descriptor of the therapy associated with the matching reference profile to the caregiver, thereby selecting a therapy for said subject.

57. An isolated nucleic acid molecule comprising iniron I substantially as hereinbefore described with reference to any one of the examples.

58. A method for preventing or treating Alzheimler's disease in a subject substantially as hereinbefore described with reference to any one of the examples.

59. A method for modulating expression, production, or formation of smyloid precursor protein (APP) in a subject. A method for selectively inhibiting COX-3 or POOX-la activity in a subject substantially as hereinbefore described with reference to any one of the examples. 7663 60-1 JIM COMS ID No: SBMI-07118661 Received by IP Australia: Time (H:rn) 16:39 Date 2007-04-24 24. APR. 2007 16:39 SPRUSON FERGUSON 92615486 NO. 7698 P. 19/19 94 0 S61. An article of maufacture comprising packgng material, a compound that modulates the activity of COX-1 variant substantially as hereinbefore described with reference to any one of the examples,

62. An t aray comprising a substrate having a plurality of addresses substantially as hereinbefore described with reference to any one of the examples.

63. A method of choosing a therapy for a subject substantially as hereinbefore described with reference to any one of the examples.

64. A kit for evaluating a pharmacetcal comprising substantially as hereinbefore en described with reference to any one of the examples. C

65. A method for selecting a therapy for a subject substantially as hereinbefore o described with reference to any one of the examples. Dated 24 April 2007 Brigham Young University 0 Patent Attorneys for the Applicant/Nominated Person SPRUSON FERGUSON 766360_1.IN COMS ID No: SBMI-07118661 Received by IP Australia: Time 16:39 Date 2007-04-24